NESG Wiki - User contributions [en]

https://nesgwiki.chem.buffalo.edu/api.php?action=feedcontributions&feedformat=atom&user=JohnEverett NESG Wiki - User contributions [en] 2026-04-09T06:50:08Z User contributions MediaWiki 1.38.2 https://nesgwiki.chem.buffalo.edu/index.php?title=DNA_cloning_protocols&diff=3027 DNA cloning protocols 2009-12-03T18:23:37Z

<p>JohnEverett: </p> <hr /> <div>== Typical Rutger's University Cloning Protocol for Target Proteins ==<br /> <br /> '''Target Selection''' <br /> <br /> Protein targets are selected based on target selection criteria. See [[Target selection]] page. <br> <br /> <br /> <br /> <br /> '''Construct design ''' <br /> <br /> Multiple constructs (typically 2-3) are designed for each full length target and targeted domains within targets.&nbsp; Constructs are designed with <br>developing automated construct design software which employs homology to the PDB, secondary structure predictions, and disorder predictions.&nbsp; <br>Predicted signal peptides are removed from auto-generated constructs.&nbsp; If a target is predicted to be extra-cellular, only constructs with one <br>or no cysteines are generated since extra-cellular proteins often require disulfide bonds for stability and proper folding that are not readily <br>formed with the NESG's ''E. coli'' cytosolic expression systems.&nbsp; Predicted transmembrane helices are removed from auto-generated constructs. <br /> <br /> <br> <br /> <br /> '''PCR&nbsp;primers and vectors ''' <br /> <br /> PCR&nbsp;primers are designed using the NESG's PCR&nbsp;primer design software ( [http://www-nmr.cabm.rutgers.edu/bioinformatics/Primer_Primer/ Primer Prim’er] <ref>Everett JK, Acton, TB, Montelione, GT.(2004) Primer prim'er: a web baased server for automated primer design. J Struct Funct Genom 5: 13-21. </ref> ) for insertion into pET15 or pET21 (Invitrogen) expression vector <br>derivatives that have amino and carboxy terminal hexa-His tags, respectively. PCR primers are designed to add 15 base pairs to the end of each PCR amplified fragment <br>desinged to pair with vectors poly-cloning region. Fusion of the PCR product and the linearized vector is performed using the Clontech In-Fusion<sup>TM</sup> PCR Cloning System.<br> <br> <br /> <br /> == References ==<br /> <br /> <references /></div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=DNA_cloning_protocols&diff=3026 DNA cloning protocols 2009-12-03T18:23:25Z

<p>JohnEverett: </p> <hr /> <div>== Typical Rutger's University Cloning Protocol for Target Proteins ==<br /> <br /> '''Target Selection''' <br /> <br /> Protein targets are selected based on target selection criteria. See [[Target selection]] page. <br><br /> <br /> '''Construct design ''' <br /> <br /> Multiple constructs (typically 2-3) are designed for each full length target and targeted domains within targets.&nbsp; Constructs are designed with <br>developing automated construct design software which employs homology to the PDB, secondary structure predictions, and disorder predictions.&nbsp; <br>Predicted signal peptides are removed from auto-generated constructs.&nbsp; If a target is predicted to be extra-cellular, only constructs with one <br>or no cysteines are generated since extra-cellular proteins often require disulfide bonds for stability and proper folding that are not readily <br>formed with the NESG's ''E. coli'' cytosolic expression systems.&nbsp; Predicted transmembrane helices are removed from auto-generated constructs. <br /> <br /> <br> <br /> <br /> '''PCR&nbsp;primers and vectors ''' <br /> <br /> PCR&nbsp;primers are designed using the NESG's PCR&nbsp;primer design software ( [http://www-nmr.cabm.rutgers.edu/bioinformatics/Primer_Primer/ Primer Prim’er] <ref>Everett JK, Acton, TB, Montelione, GT.(2004) Primer prim'er: a web baased server for automated primer design. J Struct Funct Genom 5: 13-21. </ref> ) for insertion into pET15 or pET21 (Invitrogen) expression vector <br>derivatives that have amino and carboxy terminal hexa-His tags, respectively. PCR primers are designed to add 15 base pairs to the end of each PCR amplified fragment <br>desinged to pair with vectors poly-cloning region. Fusion of the PCR product and the linearized vector is performed using the Clontech In-Fusion<sup>TM</sup> PCR Cloning System.<br> <br> <br /> <br /> == References ==<br /> <br /> <references /></div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=DNA_cloning_protocols&diff=3025 DNA cloning protocols 2009-12-03T18:23:13Z

<p>JohnEverett: </p> <hr /> <div>== Typical Rutger's University Cloning Protocol for Target Proteins ==<br /> <br /> '''Target Selection'''<br /> <br /> Protein targets are selected based on target selection criteria. See [[Target selection]] page. <br> <br /> <br /> '''Construct design ''' <br /> <br /> Multiple constructs (typically 2-3) are designed for each full length target and targeted domains within targets.&nbsp; Constructs are designed with <br>developing automated construct design software which employs homology to the PDB, secondary structure predictions, and disorder predictions.&nbsp; <br>Predicted signal peptides are removed from auto-generated constructs.&nbsp; If a target is predicted to be extra-cellular, only constructs with one <br>or no cysteines are generated since extra-cellular proteins often require disulfide bonds for stability and proper folding that are not readily <br>formed with the NESG's ''E. coli'' cytosolic expression systems.&nbsp; Predicted transmembrane helices are removed from auto-generated constructs. <br /> <br /> <br> <br /> <br /> '''PCR&nbsp;primers and vectors ''' <br /> <br /> PCR&nbsp;primers are designed using the NESG's PCR&nbsp;primer design software ( [http://www-nmr.cabm.rutgers.edu/bioinformatics/Primer_Primer/ Primer Prim’er] <ref>Everett JK, Acton, TB, Montelione, GT.(2004) Primer prim'er: a web baased server for automated primer design. J Struct Funct Genom 5: 13-21. </ref> ) for insertion into pET15 or pET21 (Invitrogen) expression vector <br>derivatives that have amino and carboxy terminal hexa-His tags, respectively. PCR primers are designed to add 15 base pairs to the end of each PCR amplified fragment <br>desinged to pair with vectors poly-cloning region. Fusion of the PCR product and the linearized vector is performed using the Clontech In-Fusion<sup>TM</sup> PCR Cloning System.<br> <br /> <br><br /> == References ==<br /> <br /> <references /></div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=DNA_cloning_protocols&diff=3000 DNA cloning protocols 2009-12-03T17:16:15Z

<p>JohnEverett: </p> <hr /> <div>== Typical Rutger's University Cloning Protocol for Target Proteins ==<br /> <br /> 1. Target Selection. <br /> <br /> Protein targets are determined based on target selection criteria. See [[Target selection]] page. <br> <br /> <br /> <br> <br /> <br /> 2. Construct design <br /> <br /> Multiple constructs (typically 2-3) are designed for each full length target and targeted domains within targets.&nbsp; Constructs are designed with <br>developing automated construct design software which employs homology to the PDB, secondary structure predictions, and disorder predictions.&nbsp; <br>Precdicted singal peptides are removed from auto-generated constructs.&nbsp; If a target is predicted to be extra-cellular, only constructs with one <br>or no cystines are generated since extra-cellular proteins often require disulfide bonds for stability and propoer folding which are not readily <br>formed with the NESG's E. coli cytosolic expression systems.&nbsp; Predicted transmembrane helices are removed from auto-generated constructs. <br /> <br /> <br> <br /> <br /> 3. PCR&nbsp;primers and vectors <br /> <br /> PCR&nbsp;primers are designed using the NESG's PCR&nbsp;primer design software ( [http://www-nmr.cabm.rutgers.edu/bioinformatics/Primer_Primer/ Primer Prim’er] <ref>Everett JK, Acton, TB, Montelione, GT.(2004) Primer prim'er: a web baased server for automated primer design. J Struct Funct Genom 5: 13-21. </ref> ) for insertion into pET15 or pET21 (Invitrogen) expression vector <br>derivatives that have amino and carboxy terminal hexa-His tags, respectively. PCR primers are designed to add 15 base pairs to the end of each PCR amplified fragment <br>desinged to pair with vectors poly-cloning region. Fusion of the PCR product and the linearized vector is performed using the Clontech In-Fusion<sup>TM</sup> PCR Cloning System.<br> <br /> <br /> <br> <br /> <br /> == Typical University of Toronto Cloning Protocol ==<br /> <br /> Coming soon... <br /> <br /> == References ==<br /> <br /> <references /></div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=DNA_cloning_protocols&diff=2989 DNA cloning protocols 2009-12-03T15:54:29Z

<p>JohnEverett: </p> <hr /> <div>== Typical Rutger's University Cloning Protocol for Target Proteins ==<br /> <br /> 1. Target Selection. <br /> <br /> Protein targets are determined based on target selection criteria. See [[Target selection]] page. <br> <br /> <br /> <br> <br /> <br /> 2. Construct design <br /> <br /> Multiple constructs (typically 2-3) are designed for each full length target and targeted domains within targets.&nbsp; Constructs are designed with <br>developing automated construct design software which employs homology to the PDB, secondary structure predictions, and disorder predictions.&nbsp; <br>Precdicted singal peptides are removed from auto-generated constructs.&nbsp; If a target is predicted to be extra-cellular, only constructs with one <br>or no cystines are generated since extra-cellular proteins often require disulfide bonds for stability and propoer folding which are not readily <br>formed with the NESG's E. coli cytosolic expression systems.&nbsp; Predicted transmembrane helices are removed from auto-generated constructs. <br /> <br /> <br> <br /> <br /> 3. PCR&nbsp;primers and vectors <br /> <br /> PCR&nbsp;primers are designed using the NESG's PCR&nbsp;primer design software ( [http://www-nmr.cabm.rutgers.edu/bioinformatics/Primer_Primer/ Primer Prim’er] <ref>Everett JK, Acton, TB, Montelione, GT.(2004) Primer prim'er: a web baased server for automated primer design. J Struct Funct Genom 5: 13-21. </ref> ) for insertion into pET15 or pET21 (Invitrogen) expression vector <br>derivatives that have amino and carobxy terminal hexa-His tags, respectively. PCR primers are designed to add 15 base pairs to the end of each PCR amplified fragment <br>desinged to pair with vectors poly-cloning region. Fusion of the PCR product and the linearized vector is performed using the Clontech In-Fusion<sup>TM</sup> PCR Cloning System.<br> <br /> <br /> <br> <br /> <br /> == Typical University of Toronto Cloning Protocol ==<br /> <br /> Coming soon... <br /> <br /> == References ==<br /> <br /> <references /></div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=DNA_cloning_protocols&diff=2988 DNA cloning protocols 2009-12-03T15:52:17Z

<p>JohnEverett: </p> <hr /> <div>== Typical Rutger's University Cloning Protocol for Target Proteins ==<br /> <br /> 1. Target Selection. <br /> <br /> Protein targets are determined based on target selection criteria. See [[Target selection]] page. <br> <br /> <br /> <br> <br /> <br /> 2. Construct design <br /> <br /> Multiple constructs (typically 2-3) are designed for each full length target and targeted domains within targets.&nbsp; Constructs are designed with <br>developing automated construct design software which employs homolog to the PDB, secondary structure predictions, and disorder predictions.&nbsp; <br>Precdicted singal peptides are removed from auto-generated constructs.&nbsp; If a target is predicted to be extra-cellular, only constructs with one <br>or no cystines are generated since extra-cellular proteins often require disulfide bonds for stability and propoer folding which are not readily <br>formed with the NESG's E. coli cytosolic expression systems.&nbsp; Predicted transmembrane helices are removed from auto-generated constructs. <br /> <br /> <br> <br /> <br /> 3. PCR&nbsp;primers and vectors <br /> <br /> PCR&nbsp;primers are designed using the NESG's PCR&nbsp;primer design software ( [http://www-nmr.cabm.rutgers.edu/bioinformatics/Primer_Primer/ Primer Prim’er] <ref>Everett JK, Acton, TB, Montelione, GT.(2004) Primer prim'er: a web baased server for automated primer design. J Struct Funct Genom 5: 13-21. </ref> ) for insertion into pET15 or pET21 (Invitrogen) expression vector <br>derivatives that have amino and carobxy terminal hexa-His tags, respectively. PCR primers are designed to add 15 base pairs to the end of each PCR amplified fragment <br>desinged to pair with vectors poly-cloning region. Fusion of the PCR product and the linearized vector is performed using the Clontech In-Fusion<sup>TM</sup> PCR Cloning System.<br> <br /> <br /> <br> <br /> <br /> == Typical University of Toronto Cloning Protocol ==<br /> <br /> Coming soon... <br /> <br /> == References ==<br /> <br /> <references /></div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=DNA_cloning_protocols&diff=2987 DNA cloning protocols 2009-12-03T15:42:45Z

<p>JohnEverett: </p> <hr /> <div>== Typical Rutger's University Cloning Protocol for Target Proteins ==<br /> <br /> 1. Target Selection. <br /> <br /> Protein targets are determined based on target selection criteria. See [[Target selection]] page. <br> <br /> <br /> <br> <br /> <br /> 2. Construct design <br /> <br /> Multiple constructs (typically 2-3) are designed for each full length target and targeted domains within targets.&nbsp; Constructs are designed with <br>developing automated construct design software which employs homolog to the PDB, secondary structure predictions, and disorder predictions.&nbsp; <br>Precdicted singal peptides are removed from auto-generated constructs.&nbsp; If a target is predicted to be extra-cellular, only constructs with one <br>or no cystines are generated since extra-cellular proteins often require disulfide bonds for stability and propoer folding which are not readily <br>formed with the NESG's E. coli cytosolic expression systems.&nbsp; Predicted transmembrane helices are removed from auto-generated constructs. <br /> <br /> <br> <br /> <br /> 3. PCR&nbsp;primers and vectors <br /> <br /> PCR&nbsp;primers are designed using the NESG's PCR&nbsp;primer design software( [http://www-nmr.cabm.rutgers.edu/bioinformatics/Primer_Primer/ Primer Prim’er] <ref>Everett JK, Acton, TB, Montelione, GT.(2004) Primer prim'er: a web baased server for automated primer design. J Struct Funct Genom 5: 13-21. </ref> ) and cloned into either pET15 or pET21 (Invitrogen) expression vector derivatives that have N- and C-terminal hexaHis tags, respectively. The primers are designed to add 15 base pairs to the end of each PCR amplified fragment that will match with the corresponding multiple cloning sites in the vector. Fusion of the PCR product and the linearized vector is performed using the Clontech In-Fusion<sup>TM</sup> PCR Cloning System.<br> <br /> <br /> <br> <br /> <br /> == Typical University of Toronto Cloning Protocol ==<br /> <br /> Coming soon... <br /> <br /> == References ==<br /> <br /> <references /></div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=DNA_cloning_protocols&diff=2986 DNA cloning protocols 2009-12-03T15:33:02Z

<p>JohnEverett: </p> <hr /> <div>== Typical Rutger's University Cloning Protocol for Target Proteins ==<br /> <br /> 1. Target Selection. <br /> <br /> Protein targets are determined based on target selection criteria. See [[Target selection]] page. <br> <br /> <br /> <br /> <br /> 2. Construct design <br /> <br /> Multiple constructs (typically 2-6) are designed for each full length target and targeted domains within targets.&nbsp; Constructs are designed with <br>developing automated construct design software which employs homolog to the PDB, secondary structure predictions, and disorder predictions.&nbsp; <br>Precdicted singal peptides are removed from auto-generated constructs.&nbsp; If a target is predicted to be extra-cellular, only constructs with one <br>or no cystines are generated since extra-cellular proteins often require disulfide bonds for stability and propoer folding which are not readily <br>formed with the NESG's E. coli cytosolic expression systems.&nbsp; Predicted transmembrane helices are removed from auto-generated constructs.<br /> <br /> <br> <br /> <br /> 3. Primers and vectors <br /> <br /> Primers are designed using [http://www-nmr.cabm.rutgers.edu/bioinformatics/Primer_Primer/ Primer Prim’er] <ref>Everett JK, Acton, TB, Montelione, GT.(2004) Primer prim'er: a web baased server for automated primer design. J Struct Funct Genom 5: 13-21. </ref> and cloned into either pET15 or pET21 (Invitrogen) expression vector derivatives that have N- and C-terminal hexaHis tags, respectively. The primers are designed to add 15 base pairs to the end of each PCR amplified fragment that will match with the corresponding multiple cloning sites in the vector. Fusion of the PCR product and the linearized vector is performed using the Clontech In-Fusion<sup>TM</sup> PCR Cloning System.<br> <br /> <br /> <br> <br /> <br /> == Typical University of Toronto Cloning Protocol ==<br /> <br /> Coming soon... <br /> <br /> == References ==<br /> <br /> <references /></div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2686 Target selection 2009-12-01T19:54:34Z

<p>JohnEverett: </p> <hr /> <div><br>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families selected by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the <span>academic</span> community and 30%&nbsp;to its own <span>biomedicaly</span> oriented projects such as key proteins in [http://nesg.org:9090/HCPIN/index.jsp Human cancer interaction<br>networks] and bacterial lipoproteins. <br /> <br /> Throughout PSI-2, protein families proposed by the PSI&nbsp;BIG&nbsp;group have been selected by the PSI-2 large scale centers via a lottery system overseen by the <br>PSI&nbsp;BIG&nbsp;group.&nbsp; Members of protein families selected by the BIG&nbsp;group are studied by the large scale centers prior to family selection and each center proposes<br>families that they wish to pursue.&nbsp; The PSI&nbsp;BIG&nbsp;group <span>resolves</span> conflicts where more than one large scale center <span>proposes</span> the same protein family. <br /> <br /> Before selecting a protein family, the NESG evaluates family members with a number of <span>predictors</span>: <br /> <br /> *[http://nmr.cabm.rutgers.edu:8080/PXS/calculatePXS.jsp Pxs] <br /> *[http://www.cbs.dtu.dk/services/SignalP/ signalP] <br /> *[http://www.cbs.dtu.dk/services/LipoP/ lipoP] <br /> *[http://www.cbs.dtu.dk/services/TMHMM/ TMHMM] <br /> *[http://www.predictprotein.org/ PredictProtein] <br /> *[http://bioinf.cs.ucl.ac.uk/disopred/ disopred2]<br /> <br /> <br> <br /> <br /> Results of PSI-2 protein family drafts: <br /> <br /> *[http://psi-big4.org/target/draft_2005-10/ Draft pick of 1369 Pfam families (Oct 2005)] <br /> *[http://psi-big4.org/target/draft_2006-04/ Draft pick of 397 BIG families (Apr 2006)] <br /> *[http://psi-big4.org/target/draft_2006-08/ Draft pick of 460 BIG families (Aug 2006)] <br /> *[http://psi-big4.org/target/draft_2006-11/ Draft pick of 602 BIG families (Nov 2006)] <br /> *[http://psi-big4.org/target/small_mega_2007-03/ Selection of 3 small MEGA families (March 2007)] <br /> *[http://psi-big4.org/target/draft_2007-05/ First round draft pick of p-loop super MEGA (May 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06/ Second round draft pick of p-loop super MEGA (June 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06_gut/ First round META genome draft pick (June 2007)] <br /> *[http://psi-big4.org/target/small_mega_2007-06/ Selection of 4 small MEGA families (June 2007)] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ Draft selection of 4 mid size MEGA families (Dec 2007)<br>] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.720/ Draft pick of NAD(P)-binding Rossmann domain (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.20.20.70/ Draft pick of Aldolase Class I (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.150/ Draft pick of VP39 (Dec 2007)] <br /> *[http://psi-big4.org/target/draft_2008-05/ Draft pick of 1000 MEGA modeling families (250/center) (May 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07/ Draft pick of 136 META HMM families (34/center) (July 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07_mega/ Draft pick of 1000 MEGA modeling families (250/center) (July 2008)]</div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2685 Target selection 2009-12-01T19:53:52Z

<p>JohnEverett: </p> <hr /> <div><br>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families selected by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the <span>academic</span> community and 30%&nbsp;to its own <span>biomedicaly</span> oriented projects such as key proteins in [http://nesg.org:9090/HCPIN/index.jsp Human cancer interaction<br>networks] and bacterial lipoproteins. <br /> <br /> Throughout PSI-2, protein families proposed by the PSI&nbsp;BIG&nbsp;group have been selected by the PSI-2 large scale centers via a lottery system overseen by the <br>PSI&nbsp;BIG&nbsp;group.&nbsp; Members of protein families selected by the BIG&nbsp;group are studied by the large scale centers prior to family selection and each center proposes<br>families that they wish to pursue.&nbsp; The PSI&nbsp;BIG&nbsp;group <span>resolves</span> conflicts where more than one large scale center <span>proposes</span> the same protein family. <br /> <br /> Before selecting a protein family, the NESG evaluates family members with a number of <span>predictors</span>: <br /> <br /> *[http://nmr.cabm.rutgers.edu:8080/PXS/calculatePXS.jsp Pxs] <br /> *[http://www.cbs.dtu.dk/services/SignalP/ signalP] <br /> *[http://www.cbs.dtu.dk/services/LipoP/ lipoP] <br /> *[http://www.cbs.dtu.dk/services/TMHMM/ TMHMM] <br /> *[http://www.predictprotein.org/ PredictProtein] <br /> *[http://bioinf.cs.ucl.ac.uk/disopred/ disopred2]<br /> <br /> <br> <br /> <br /> Result of PSI-2 protein family drafts: <br /> <br /> *[http://psi-big4.org/target/draft_2005-10/ Draft pick of 1369 Pfam families (Oct 2005)] <br /> *[http://psi-big4.org/target/draft_2006-04/ Draft pick of 397 BIG families (Apr 2006)] <br /> *[http://psi-big4.org/target/draft_2006-08/ Draft pick of 460 BIG families (Aug 2006)] <br /> *[http://psi-big4.org/target/draft_2006-11/ Draft pick of 602 BIG families (Nov 2006)] <br /> *[http://psi-big4.org/target/small_mega_2007-03/ Selection of 3 small MEGA families (March 2007)] <br /> *[http://psi-big4.org/target/draft_2007-05/ First round draft pick of p-loop super MEGA (May 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06/ Second round draft pick of p-loop super MEGA (June 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06_gut/ First round META genome draft pick (June 2007)] <br /> *[http://psi-big4.org/target/small_mega_2007-06/ Selection of 4 small MEGA families (June 2007)] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ Draft selection of 4 mid size MEGA families (Dec 2007)<br>] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.720/ Draft pick of NAD(P)-binding Rossmann domain (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.20.20.70/ Draft pick of Aldolase Class I (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.150/ Draft pick of VP39 (Dec 2007)] <br /> *[http://psi-big4.org/target/draft_2008-05/ Draft pick of 1000 MEGA modeling families (250/center) (May 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07/ Draft pick of 136 META HMM families (34/center) (July 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07_mega/ Draft pick of 1000 MEGA modeling families (250/center) (July 2008)]</div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2684 Target selection 2009-12-01T19:52:32Z

<p>JohnEverett: </p> <hr /> <div><br>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families assigned by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the <span>academic</span> community and 30%&nbsp;to its own <span>biomedicaly</span> oriented projects such as key proteins in [http://nesg.org:9090/HCPIN/index.jsp Human cancer interaction<br>networks] and bacterial lipoproteins. <br /> <br /> Throughout PSI-2, protein families proposed by the PSI&nbsp;BIG&nbsp;group have been selected by the PSI-2 large scale centers via a lottery system overseen by the <br>PSI&nbsp;BIG&nbsp;group.&nbsp; Members of protein families selected by the BIG&nbsp;group are studied by the large scale centers prior to family selection and each center proposes<br>families that they wish to pursue.&nbsp; The PSI&nbsp;BIG&nbsp;group <span>resolves</span> conflicts where more than one large scale center <span>proposes</span> the same protein family. <br /> <br /> Before selecting a protein family, the NESG evaluates family members with a number of <span>predictors</span>: <br /> <br /> *[http://nmr.cabm.rutgers.edu:8080/PXS/calculatePXS.jsp Pxs] <br /> *[http://www.cbs.dtu.dk/services/SignalP/ signalP] <br /> *[http://www.cbs.dtu.dk/services/LipoP/ lipoP] <br /> *[http://www.cbs.dtu.dk/services/TMHMM/ TMHMM] <br /> *[http://www.predictprotein.org/ PredictProtein] <br /> *[http://bioinf.cs.ucl.ac.uk/disopred/ disopred2]<br /> <br /> <br> <br /> <br /> Result of PSI-2 protein family drafts: <br /> <br /> *[http://psi-big4.org/target/draft_2005-10/ Draft pick of 1369 Pfam families (Oct 2005)] <br /> *[http://psi-big4.org/target/draft_2006-04/ Draft pick of 397 BIG families (Apr 2006)] <br /> *[http://psi-big4.org/target/draft_2006-08/ Draft pick of 460 BIG families (Aug 2006)] <br /> *[http://psi-big4.org/target/draft_2006-11/ Draft pick of 602 BIG families (Nov 2006)] <br /> *[http://psi-big4.org/target/small_mega_2007-03/ Selection of 3 small MEGA families (March 2007)] <br /> *[http://psi-big4.org/target/draft_2007-05/ First round draft pick of p-loop super MEGA (May 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06/ Second round draft pick of p-loop super MEGA (June 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06_gut/ First round META genome draft pick (June 2007)] <br /> *[http://psi-big4.org/target/small_mega_2007-06/ Selection of 4 small MEGA families (June 2007)] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ Draft selection of 4 mid size MEGA families (Dec 2007)<br>] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.720/ Draft pick of NAD(P)-binding Rossmann domain (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.20.20.70/ Draft pick of Aldolase Class I (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.150/ Draft pick of VP39 (Dec 2007)] <br /> *[http://psi-big4.org/target/draft_2008-05/ Draft pick of 1000 MEGA modeling families (250/center) (May 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07/ Draft pick of 136 META HMM families (34/center) (July 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07_mega/ Draft pick of 1000 MEGA modeling families (250/center) (July 2008)]</div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Wiki_Tree_Layout&diff=2653 Wiki Tree Layout 2009-12-01T17:39:09Z

<p>JohnEverett: </p> <hr /> <div>This outline of the NESG NMR Wiki is designed to expand on the existing "Master Recipe" and should serve as an experience harvesting tool. <br /> <br /> *It has a rather broad coverage to facilitate long-tewrm growth and development. Aditional compact aggregator pages may be needed to pesent specific information concisely. <br /> *There would be separate webs within the wiki: Public(or Main), NESG, and member lab webs. Most common knowlege topics should be public, unless they are specific to NESG <br /> *We assume that the target audience has some knowledge about NMR and protein structure determination, but make the content useful for training <br /> *"Resonance Assignment" and "Structure Determination" chaptes would focus on individual software packages. The XEASY resonance assignment tree, as the most complete, would serve as a template for other software. <br /> *Most chapters should include a "general principles" section.<br /> <br /> Please leave your comments/suggestion at the bottom of this page <br /> <br /> <br> <br /> <br /> = HTP NMR structure determination =<br /> <br /> == Protein Target Selection, Sample Preparation, and Initial Screening ==<br /> <br /> #[[Target selection|NESG target selection]] <br><br /> #[[DNA cloning protocols|DNA cloning protocols]]<br> <br /> #[[Protein purification|Protein expression and purification protocols]]&nbsp;<br> <br /> #Sample Optimization <br /> ##[[Construct optimization]] <br /> ##[[Buffer optimization]] <br /> ##[[Cofactor optimization]] <br /> #Initial protein analysis <br /> ##[[SDS page gel]] <br /> ##[[Protein concentration|Protein concentration measurements]] <br /> ##[[Oligomerization Status|Assessment of Oligomerization Status]] <br /> ###[[Gel filtration and light scattering|gel-filtration and light scattering]] <br /> ###[[NMR determined Rotational correlation time]] <br /> ##[[MassSpectrometry|Mass spectrum]] <br /> ##NMR screening <br /> ###[[1D screening|<sup>1</sup>H 1D screening]] <br /> ###[[Nhsqc screen|Initial [<sup>15</sup>N,<sup>1</sup>H] HSQC]]<br><br /> <br /> == NMR Data Collection ==<br /> <br /> #Routine operation <br /> ##[[NMR sample tubes]] <br /> ##[[NMR Sample Preparation]] <br /> ##[[Inserting NMR Sample]] <br /> ##Tuning and matching <br /> ##[[Deuterium Lock]] <br /> ##[[Shimming]] <br /> ##[[Pulse width calibration]] <br /> ##[[Temperature calibration]] <br /> ##[[Chemical shift referencing]] <br /> #Advanced operation <br /> ##[[Deuterium pulse width calibration and decoupling]] <br /> #NMR data acquisition for protein structure determination <br /> ##[[Common NMR experiment sets]] <br /> ##[[NMR experiment setup scripts for VNMRJ|Custom NMR experiment setup scripts for VNMRJ]] <br /> ##1D 1H NMR spectra and 2D [15N, 1H]-HSQC <br /> ##[[Estimation of rotational correlation time]] <br /> ##[[Estimation of measurement time]] <br /> ##NMR experiments for spin system identification <br /> ##2D and 3D NOESY experiments <br /> ###[[Simultaneous 13C,15N-resolved NOESY]] <br /> ##Double and triple NMR experiments <br /> ###3D CBCA(CO)NH and HNCACB <br /> ###3D HNCA and HN(CO)CA <br /> ###3D HAHB(CO)NH <br /> ###(4,3)D CABCA(CO)NH and HNCACB <br /> ###(4,3)D HABCAB(CO)NH <br /> ###(H)CCH <br /> ###(H)CCH-TOCSY <br /> ###H(C)CH <br /> ###H(C)CH-TOCSY <br /> ###(4,3)D HCCH <br /> ##Other NMR experiments <br /> ###[[2D (13C, 1H) HSQC for fractionally 13C-labeled samples|2D [13C, 1H]-HSQC for fractionally 13C-labeled samples]] <br /> ###[[Long-range 15N-1H correlation experiments for histidine rings]] - determination of histidine isoprotomer state <br /> ###MEXICO <br /> ###CLEANEX <br /> ###H-D exchange experiment <br /> ###15N spin relaxation parameters <br /> #Advanced problems for data collection <br /> ##[[Setting up non-uniformly sampled spectra]] <br /> ###[[Setting up non-uniformly sampled spectra/NUS guide for Varian|Guide for Varian/BioPack]] <br /> ###[[Setting up non-uniformly sampled spectra/NUS guide for Bruker according to Arrowsmith group in Toronto|Guide for Bruker/Topspin according to Arrowsmith group]] <br /> #Maintenance <br /> ##VARIAN <br /> ###[[Installing and updating BioPack]] <br /> ###[[Full probefile calibration]] <br /> ###[[Rebooting spectrometer console]] <br /> ###[[Conditioning procedure for cryogenic probes]] <br /> ##BRUKER<br /> <br /> == NMR Data Processing ==<br /> <br /> #General Priciples and Concepts <br /> ##Fourier transformation <br /> ###Zero-filling <br /> ###Apodization <br /> ###Phasing <br /> ###Linear prediction <br /> ###G-matrix Fourier transformation (GFT) <br /> ##Alternatives to Fourier transformation <br /> ###Maximum entropy reconstruction <br /> ###[[Processing non-uniformly sampled spectra with Multidimensional Decomposition]] <br /> ###... <br /> #Practical Aspects <br /> ##NMRPIPE <br /> ###<font color="#000000">General information</font> <br /> ###<font color="#0000ff">Buffalo's Processing Protocol using NMRpipe</font> <br /> ##[[Processing NMR spectra with PROSA|PROSA]] <br /> ##TOPSPIN <br /> ##[[AGNuS/AutoProc|AGNuS/AutoProc]] <br /> ##UBNMR <br /> ##Spectral format conversion<br /> <br /> <br> <br /> <br /> == [[Resonance Assignment]] ==<br /> <br /> This chapter focuses on data analysis and resonance assignment packages, as most people stick to a particular software for entire structure determination projects. <br /> <br /> <br> <br /> <br /> #[[Resonance Assignment/Principles and concepts|Principles and concepts]] <br /> #[[Resonance Assignmet/Practical aspects|Practical aspects]] <br /> ##[[Resonance Assignment/Semi-automated protocols|Semi-automated protocols]] <br /> ###[[CARA]] <br /> ####[[Spin System Identification with CARA|Spin System Identification in 2D 15N-HSQC and 3D HNNCO]] <br /> ####[[Backbone Assignment with CARA|Backbone Resonance Assignment]] <br /> ####[[HA and HB Assignment with CARA|Assignment of HA and HB Resonances with (4,3)D GFT HABCAB(CO)NHN]] <br /> ####Side Chain Assignment <br /> #####[[Aliphatic Side Chain Assignment with CARA|Aliphatic side-chain assignment]] <br /> #####[[Aromatic Side Chain Assignment with CARA|Aromatic side-chain assignment]] <br /> #####[[Amide Side Chain Assignment with CARA|Amide side-chain assignment]] <br /> ###[[Sparky]] <br /> ###[[XEASY]] <br /> ####[[XEASY Spin system identification|Spin system identification]] <br /> ####Backbone resonance assignment'''<br>''' <br /> #####GFT-based spectra <br /> ######[[HNCACAB/CABCA(CO)NH]] <br /> #####Conventional spectra <br /> ######[[HNCACB/CBCA(CO)NH]] <br /> ######HNCA/HN(CO)CA <br /> ######HNCO/HN(CA)CO <br /> ######NOESY/TOCSY <br /> ####[[XEASY Side Chain Assignment|Side chain resonance assignment]] <br /> #####Aliphatic <br /> ######GFT NMR spectra <br /> #######[[HA and HB Assignment with GFT in XEASY|(4,3)D GFT HABCAB(CO)NHN]] <br /> #######[[Side chain assignment with aliphatic (4,3)D HCCH-COSY in XEASY|(4,3)D GFT HCCH]] <br /> ######Conventional spectra <br /> #######HAHB(CO)NH <br /> #######HCCH-COSY <br /> #######HCCH-TOCSY <br /> #######[[Side chain assignment with CN-NOESY in XEASY|Simultaneous NOESY]] <br /> #######(H)CC-TOCSY-(CO)NH <br /> #######H(CC-TOCSY-CO)NH <br /> #####[[Aromatic side chain assignment with Aro-HCCH-COSY in XEASY|Aromatic]] <br /> ######GFT-based spectra <br /> ######Conventional spectra <br /> #####Other <br /> ######Trp e1 NH and d1 CH <br /> ######[[Met methyl assignment with NOESY|Met e CH3 ]] <br /> ######[[Amide Side Chain assignment with NOESY|Asn d2 and Gln e2 NH2]] <br /> #####NOESY peak integration <br /> ##Automated protocols <br /> ###[[AutoAssign|AutoAssign]] <br /> ###[[AutoAssign WebServer|AutoAssign server]] <br /> ###[[Abacus|ABACUS]] <br /> ###[[The PINE Server|PINE server]] <br /> ##Validation of resonance assignment <br /> ###[[AVS|Assignment validation suite (AVS)]] <br /> ###[[LACS|Linear analysis of chemical shift (LACS)]] <br /> ##[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]]<br /> <br /> <br> <br /> <br /> == Structure Calculation and Validation ==<br /> <br /> #[[Structure Calculation and Validation|Principles and concepts]] <br /> #Practical aspects <br /> ##Structure calculation <br /> ###CYANA <br /> ####[[CYANA|Getting started]] <br /> ####[[FOUND|FOUND]] <br /> ####[[TALOS|TALOS]] <br /> ####[[GLOMSA|GLOMSA]] <br /> ####[[NOE Calibration Using CYANA|NOE calibration]] <br /> ####[[Manual Structure Calculation Using CYANA|Manual structure calculation]] <br /> ####[[Automated NOESY Assignment Using CYANA|Automated NOESY assignment and structure calculation]] <br /> ####[[Structure Calculation With RDC's Using CYANA|Structure calculation with residual dipolar couplings]] (link to REDCAT/PALES,FINDTENSOR, .rdc file, adding ORI to PDB file) <br /> ####[[Homodimer Structure Calculation Using CYANA|Homodimer structure calculations]][[Homodimer Structure Calculation Using CYANA|<br>]] <br /> ###AutoStructure <br /> ####[[AutoStructure/RPF Theory|Theory]] <br /> ####[[AutoStructure|Getting started]] <br /> ####[[CYANA Structure Calculations Using AutoStructure|CYANA run]] <br /> ####[[XPLOR Structure Calculations Using AutoStructure|XPLOR run]] <br /> ####[[Analyzing AutoStructure Output Directories|Analyzing the output]] <br /> ####[[RPF Analysis|RPF/DP scores]] <br /> ####[[Structure Calculation Using AS-DP|Structure calculation using AS-DP]] <br /> ###"Consensus"&nbsp;Approaches <br /> ####[[Overview of Consensus Runs|Overview of Consensus runs]] <br /> ####[[Finding Consensus NOE Assignments|Finding Consensus NOE assignments]] <br /> ####[[Validation of Consensus Run|Validation of Consensus runs]] <br /> ###[[Structure Calculation Using CS-Rosetta|CS-ROSETTA]] <br /> ###[[Structure Calculation Using CS-DP ROSETTA|CS-DP ROSETTA]] <br /> ###[[Structure Calculation Using RDC-ROSETTA|RDC-ROSETTA]] <br /> ###[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]<br> <br /> ###Special topics <br /> ####[[Protein-Ligand Complexes|Protein-Ligand complexes]] <br /> ####[[Working With Metal Ions|Metal ions]] <br /> ####[[Working With Dimers|Dimers]] <br /> ####[[Residual Dipolar Couplings in Structure Refinement|Residual Dipolar Couplings]] <br /> ####[[REDCAT|REDCAT]]&nbsp;and [[REDCRAFT|REDCRAFT]] <br /> ####[[Paramagnetic Constraints in Structure Determination|Paramagnetic constraints]] <br /> ##Structure Refinement <br /> ###[[Structure Refinement Using CNS Energy Minimization With Explicit Water|CNS refinement]] <br /> ###[[Structure Refinement Using XPLOR-NIH|XPLOR-NIH refinement]] <br /> ###[[Rosetta High Resolution Protein Structure Refinement Protocol|ROSETTA refinement]] <br /> ##Validation and deposition <br /> ###[[PdbStat|PdbStat]] <br /> ###[[PSVS|PSVS]] <br /> ###[[RPF Analysis|RPF analysis]] <br /> ###[[MolProbity Server|MolProbity server]] <br /> ###[[PDB and BMRB Deposition|PDB and BMRB deposition]] <br /> ###[[ADIT-NMR|ADIT-NMR]] <br /> ###[[HarvestDB|HarvestDB]] <br /> ###[[SPINS|SPINS]]<br /> <br /> -- JeffMills - 28 May 2009 <br /> <br /> Here are two comments from Guy: <br /> <br /> - need to have centralized site for downloading all software that NESG has developed or licensed; this would be a central site for NESG scientists to use to access the latest version of all software <br /> <br /> - need to allow outside users to access links to all software (they will need licenses to download) and also to download software from NESG <br /> <br /> -- AlexEletski - 13 Jul 2009 <br /> <br /> &nbsp;</div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2631 Target selection 2009-12-01T17:12:28Z

<p>JohnEverett: </p> <hr /> <div><br>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families assigned by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the <span>academic</span> community and 30%&nbsp;to its own <span>biomedicaly</span> oriented projects such as key proteins in [http://nesg.org:9090/HCPIN/index.jsp Human cancer interaction<br>networks] and bacterial lipoproteins. <br /> <br /> Throughout PSI-2, protein families proposed by the PSI&nbsp;BIG&nbsp;group have been selected by the PSI-2 large scale centers via a lottery system overseen by the <br>PSI&nbsp;BIG&nbsp;group.&nbsp; Members of protein families selected by the BIG&nbsp;group are studied by the large scale centers prior to family selection and each center proposes<br>families that they wish to pursue.&nbsp; The PSI&nbsp;BIG&nbsp;group <span>resolves</span> conflicts where more than one large scale center <span>proposes</span> the same protein family. <br /> <br /> Before selecting a protein family, the NESG evaluates family members with a number of <span>predictors</span>: <br /> <br /> *[http://nmr.cabm.rutgers.edu:8080/PXS/calculatePXS.jsp Pxs] <br /> *[http://www.cbs.dtu.dk/services/SignalP/ signalP] <br /> *[http://www.cbs.dtu.dk/services/LipoP/ lipoP] <br /> *[http://www.cbs.dtu.dk/services/TMHMM/ TMHMM] <br /> *[http://www.predictprotein.org/ PredictProtein] <br /> *[http://bioinf.cs.ucl.ac.uk/disopred/ disopred2]<br /> <br /> <br> <br /> <br /> Result of PSI-2 protein family drafts: <br /> <br /> *[http://psi-big4.org/target/draft_2005-10/ Draft pick of 1369 Pfam families (Oct 2005)] <br /> *[http://psi-big4.org/target/draft_2006-04/ Draft pick of 397 BIG families (Apr 2006)] <br /> *[http://psi-big4.org/target/draft_2006-08/ Draft pick of 460 BIG families (Aug 2006)] <br /> *[http://psi-big4.org/target/draft_2006-11/ Draft pick of 602 BIG families (Nov 2006)] <br /> *[http://psi-big4.org/target/small_mega_2007-03/ Selection of 3 small MEGA families (March 2007)] <br /> *[http://psi-big4.org/target/draft_2007-05/ First round draft pick of p-loop super MEGA (May 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06/ Second round draft pick of p-loop super MEGA (June 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06_gut/ First round META genome draft pick (June 2007)] <br /> *[http://psi-big4.org/target/small_mega_2007-06/ Selection of 4 small MEGA families (June 2007)] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ Draft selection of 4 mid size MEGA families (Dec 2007)<br>] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/][http://psi-big4.org/target/super_mega_2007-12/3.40.50.720/ Draft pick of NAD(P)-binding Rossmann domain (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.20.20.70/ Draft pick of Aldolase Class I (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.150/ Draft pick of VP39 (Dec 2007)] <br /> *[http://psi-big4.org/target/draft_2008-05/ Draft pick of 1000 MEGA modeling families (250/center) (May 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07/ Draft pick of 136 META HMM families (34/center) (July 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07_mega/ Draft pick of 1000 MEGA modeling families (250/center) (July 2008)]</div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2630 Target selection 2009-12-01T17:10:46Z

<p>JohnEverett: </p> <hr /> <div><br>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families assigned by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the <span>academic</span> community and 30%&nbsp;to its own <span>biomedicaly</span> oriented projects such as key proteins in Human cancer interaction<br>networks and bacterial lipoproteins. <br /> <br /> Throughout PSI-2, protein families proposed by the PSI&nbsp;BIG&nbsp;group have been selected by the PSI-2 large scale centers via a lottery system overseen by the <br>PSI&nbsp;BIG&nbsp;group.&nbsp; Members of protein families selected by the BIG&nbsp;group are studied by the large scale centers prior to family selection and each center proposes<br>families that they wish to pursue.&nbsp; The PSI&nbsp;BIG&nbsp;group <span>resolves</span> conflicts where more than one large scale center <span>proposes</span> the same protein family. <br /> <br /> Before selecting a protein family, the NESG evaluates family members with a number of <span>predictors</span>: <br /> <br /> *[http://nmr.cabm.rutgers.edu:8080/PXS/calculatePXS.jsp Pxs] <br /> *[http://www.cbs.dtu.dk/services/SignalP/ signalP] <br /> *[http://www.cbs.dtu.dk/services/LipoP/ lipoP] <br /> *[http://www.cbs.dtu.dk/services/TMHMM/ TMHMM] <br /> *[http://www.predictprotein.org/ PredictProtein] <br /> *[http://bioinf.cs.ucl.ac.uk/disopred/ disopred2]<br /> <br /> <br> <br /> <br /> Result of PSI-2 protein family drafts: <br /> <br /> *[http://psi-big4.org/target/draft_2005-10/ Draft pick of 1369 Pfam families (Oct 2005)] <br /> *[http://psi-big4.org/target/draft_2006-04/ Draft pick of 397 BIG families (Apr 2006)] <br /> *[http://psi-big4.org/target/draft_2006-08/ Draft pick of 460 BIG families (Aug 2006)] <br /> *[http://psi-big4.org/target/draft_2006-11/ Draft pick of 602 BIG families (Nov 2006)] <br /> *[http://psi-big4.org/target/small_mega_2007-03/ Selection of 3 small MEGA families (March 2007)] <br /> *[http://psi-big4.org/target/draft_2007-05/ First round draft pick of p-loop super MEGA (May 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06/ Second round draft pick of p-loop super MEGA (June 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06_gut/ First round META genome draft pick (June 2007)] <br /> *[http://psi-big4.org/target/small_mega_2007-06/ Selection of 4 small MEGA families (June 2007)] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ Draft selection of 4 mid size MEGA families (Dec 2007)<br>] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/][http://psi-big4.org/target/super_mega_2007-12/3.40.50.720/ Draft pick of NAD(P)-binding Rossmann domain (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.20.20.70/ Draft pick of Aldolase Class I (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.150/ Draft pick of VP39 (Dec 2007)] <br /> *[http://psi-big4.org/target/draft_2008-05/ Draft pick of 1000 MEGA modeling families (250/center) (May 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07/ Draft pick of 136 META HMM families (34/center) (July 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07_mega/ Draft pick of 1000 MEGA modeling families (250/center) (July 2008)]</div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2627 Target selection 2009-12-01T17:07:51Z

<p>JohnEverett: </p> <hr /> <div>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families assigned by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the <meta content="text/html; charset=utf-8" http-equiv="Content-Type"></meta><meta content="Word.Document" name="ProgId"></meta><meta content="Microsoft Word 11" name="Generator"></meta><meta content="Microsoft Word 11" name="Originator"></meta><link href="file:///C:\Users\kellere\AppData\Local\Temp\msohtml1\01\clip_filelist.xml" rel="File-List"></link><style>&lt;!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0in; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";} @page Section1 {size:8.5in 11.0in; margin:1.0in 1.25in 1.0in 1.25in; mso-header-margin:.5in; mso-footer-margin:.5in; mso-paper-source:0;} div.Section1 {page:Section1;} --&gt; </style><span style="font-size: 12pt; font-family: &quot;Times New Roman";">academic</span> community and 30%&nbsp;to its own <meta content="text/html; charset=utf-8" http-equiv="Content-Type"></meta><meta content="Word.Document" name="ProgId"></meta><meta content="Microsoft Word 11" name="Generator"></meta><meta content="Microsoft Word 11" name="Originator"></meta><link href="file:///C:\Users\kellere\AppData\Local\Temp\msohtml1\01\clip_filelist.xml" rel="File-List"></link><style>&lt;!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0in; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";} @page Section1 {size:8.5in 11.0in; margin:1.0in 1.25in 1.0in 1.25in; mso-header-margin:.5in; mso-footer-margin:.5in; mso-paper-source:0;} div.Section1 {page:Section1;} --&gt; </style><span style="font-size: 12pt; font-family: &quot;Times New Roman";">biomedicaly</span> oriented projects such as key proteins in Human cancer interaction<br>networks and bacterial lipoproteins. <br /> <br /> Throughout PSI-2, protein families proposed by the PSI&nbsp;BIG&nbsp;group have been selected by the PSI-2 large scale centers via a lottery system overseen by the <br>PSI&nbsp;BIG&nbsp;group.&nbsp; Members of protein families selected by the BIG&nbsp;group are studied by the large scale centers prior to family selection and each center proposes<br>families that they wish to pursue.&nbsp; The PSI&nbsp;BIG&nbsp;group <meta content="text/html; charset=utf-8" http-equiv="Content-Type"></meta><meta content="Word.Document" name="ProgId"></meta><meta content="Microsoft Word 11" name="Generator"></meta><meta content="Microsoft Word 11" name="Originator"></meta><link href="file:///C:\Users\kellere\AppData\Local\Temp\msohtml1\01\clip_filelist.xml" rel="File-List"></link><style>&lt;!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0in; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";} @page Section1 {size:8.5in 11.0in; margin:1.0in 1.25in 1.0in 1.25in; mso-header-margin:.5in; mso-footer-margin:.5in; mso-paper-source:0;} div.Section1 {page:Section1;} --&gt; </style><span style="font-size: 12pt; font-family: &quot;Times New Roman";">resolves</span> conflicts where more than one large scale center <meta content="text/html; charset=utf-8" http-equiv="Content-Type"></meta><meta content="Word.Document" name="ProgId"></meta><meta content="Microsoft Word 11" name="Generator"></meta><meta content="Microsoft Word 11" name="Originator"></meta><link href="file:///C:\Users\kellere\AppData\Local\Temp\msohtml1\01\clip_filelist.xml" rel="File-List"></link><style>&lt;!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0in; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";} @page Section1 {size:8.5in 11.0in; margin:1.0in 1.25in 1.0in 1.25in; mso-header-margin:.5in; mso-footer-margin:.5in; mso-paper-source:0;} div.Section1 {page:Section1;} --&gt; </style><span style="font-size: 12pt; font-family: &quot;Times New Roman";">proposes</span> the same protein family. <br /> <br /> Before selecting a protein family, the NESG evaluates family members with a number of <meta content="text/html; charset=utf-8" http-equiv="Content-Type"></meta><meta content="Word.Document" name="ProgId"></meta><meta content="Microsoft Word 11" name="Generator"></meta><meta content="Microsoft Word 11" name="Originator"></meta><link href="file:///C:\Users\kellere\AppData\Local\Temp\msohtml1\01\clip_filelist.xml" rel="File-List"></link><style>&lt;!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0in; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";} @page Section1 {size:8.5in 11.0in; margin:1.0in 1.25in 1.0in 1.25in; mso-header-margin:.5in; mso-footer-margin:.5in; mso-paper-source:0;} div.Section1 {page:Section1;} --&gt; </style><span style="font-size: 12pt; font-family: &quot;Times New Roman";">predictors</span>: <br /> <br /> *[http://nmr.cabm.rutgers.edu:8080/PXS/calculatePXS.jsp Pxs] <br /> *[http://www.cbs.dtu.dk/services/SignalP/ signalP] <br /> *[http://www.cbs.dtu.dk/services/LipoP/ lipoP] <br /> *[http://www.cbs.dtu.dk/services/TMHMM/ TMHMM] <br /> *[http://www.predictprotein.org/ PredictProtein] <br /> *[http://bioinf.cs.ucl.ac.uk/disopred/ disopred2]<br /> <br /> <br> <br /> <br /> Result of PSI-2 protein family drafts: <br /> <br /> *[http://psi-big4.org/target/draft_2005-10/ Draft pick of 1369 Pfam families (Oct 2005)] <br /> *[http://psi-big4.org/target/draft_2006-04/ Draft pick of 397 BIG families (Apr 2006)] <br /> *[http://psi-big4.org/target/draft_2006-08/ Draft pick of 460 BIG families (Aug 2006)] <br /> *[http://psi-big4.org/target/draft_2006-11/ Draft pick of 602 BIG families (Nov 2006)] <br /> *[http://psi-big4.org/target/small_mega_2007-03/ Selection of 3 small MEGA families (March 2007)] <br /> *[http://psi-big4.org/target/draft_2007-05/ First round draft pick of p-loop super MEGA (May 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06/ Second round draft pick of p-loop super MEGA (June 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06_gut/ First round META genome draft pick (June 2007)] <br /> *[http://psi-big4.org/target/small_mega_2007-06/ Selection of 4 small MEGA families (June 2007)] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ Draft selection of 4 mid size MEGA families (Dec 2007)<br>] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/][http://psi-big4.org/target/super_mega_2007-12/3.40.50.720/ Draft pick of NAD(P)-binding Rossmann domain (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.20.20.70/ Draft pick of Aldolase Class I (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.150/ Draft pick of VP39 (Dec 2007)] <br /> *[http://psi-big4.org/target/draft_2008-05/ Draft pick of 1000 MEGA modeling families (250/center) (May 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07/ Draft pick of 136 META HMM families (34/center) (July 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07_mega/ Draft pick of 1000 MEGA modeling families (250/center) (July 2008)]</div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2626 Target selection 2009-12-01T17:05:49Z

<p>JohnEverett: </p> <hr /> <div>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families assigned by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the accademic community and 30%&nbsp;to its own biomedically oriented projects such as key proteins in Human cancer interaction<br>networks and bacterial lipoproteins. <br /> <br /> Throughout PSI-2, protein families proposed by the PSI&nbsp;BIG&nbsp;group have been selected by the PSI-2 large scale centers via a lottery system overseen by the <br>PSI&nbsp;BIG&nbsp;group.&nbsp; Members of protein families selected by the BIG&nbsp;group are studied by the large scale centers prior to family selection and each center proposes<br>families that they wish to pursue.&nbsp; The PSI&nbsp;BIG&nbsp;group resovles conflicts where more than one large scale center prposes the same protein family. <br /> <br /> Before selecting a protein family, the NESG evaluates family members with a number of predicters: <br /> <br /> *[http://nmr.cabm.rutgers.edu:8080/PXS/calculatePXS.jsp Pxs] <br /> *[http://www.cbs.dtu.dk/services/SignalP/ signalP] <br /> *[http://www.cbs.dtu.dk/services/LipoP/ lipoP] <br /> *[http://www.cbs.dtu.dk/services/TMHMM/ TMHMM] <br /> *[http://www.predictprotein.org/ PredictProtein]<br /> *[http://bioinf.cs.ucl.ac.uk/disopred/ disopred2]<br /> <br /> <br> <br /> <br /> Result of PSI-2 protein family drafts: <br /> <br /> *[http://psi-big4.org/target/draft_2005-10/ Draft pick of 1369 Pfam families (Oct 2005)] <br /> *[http://psi-big4.org/target/draft_2006-04/ Draft pick of 397 BIG families (Apr 2006)] <br /> *[http://psi-big4.org/target/draft_2006-08/ Draft pick of 460 BIG families (Aug 2006)] <br /> *[http://psi-big4.org/target/draft_2006-11/ Draft pick of 602 BIG families (Nov 2006)] <br /> *[http://psi-big4.org/target/small_mega_2007-03/ Selection of 3 small MEGA families (March 2007)] <br /> *[http://psi-big4.org/target/draft_2007-05/ First round draft pick of p-loop super MEGA (May 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06/ Second round draft pick of p-loop super MEGA (June 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06_gut/ First round META genome draft pick (June 2007)] <br /> *[http://psi-big4.org/target/small_mega_2007-06/ Selection of 4 small MEGA families (June 2007)] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ Draft selection of 4 mid size MEGA families (Dec 2007)<br>] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/][http://psi-big4.org/target/super_mega_2007-12/3.40.50.720/ Draft pick of NAD(P)-binding Rossmann domain (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.20.20.70/ Draft pick of Aldolase Class I (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.150/ Draft pick of VP39 (Dec 2007)] <br /> *[http://psi-big4.org/target/draft_2008-05/ Draft pick of 1000 MEGA modeling families (250/center) (May 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07/ Draft pick of 136 META HMM families (34/center) (July 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07_mega/ Draft pick of 1000 MEGA modeling families (250/center) (July 2008)]</div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2621 Target selection 2009-12-01T17:02:28Z

<p>JohnEverett: </p> <hr /> <div>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families assigned by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the accademic community and 30%&nbsp;to its own biomedically oriented projects such as key proteins in Human cancer interaction<br>networks and bacterial lipoproteins. <br /> <br /> Throughout PSI-2, protein families proposed by the PSI&nbsp;BIG&nbsp;group have been selected by the PSI-2 large scale centers via a lottery system overseen by the <br>PSI&nbsp;BIG&nbsp;group.&nbsp; Members of protein families selected by the BIG&nbsp;group are studied by the large scale centers prior to family selection and each center proposes<br>families that they wish to pursue.&nbsp; The PSI&nbsp;BIG&nbsp;group resovles conflicts where more than one large scale center prposes the same protein family. <br /> <br /> Before selecting a protein family, the NESG evaluates family members with a number of predicters:<br /> <br /> *Pxs<br /> *signalP<br /> *lipoP<br /> *TMHMM<br /> *PredictProtein<br /> *disopred<br /> <br /> <br /> <br /> Result of PSI-2 protein family drafts:[http://psi-big4.org/target/draft_2005-10/ ]<br /> <br /> *[http://psi-big4.org/target/draft_2005-10/ Draft pick of 1369 Pfam families (Oct 2005)]<br /> *[http://psi-big4.org/target/draft_2006-04/ Draft pick of 397 BIG families (Apr 2006)]<br /> *[http://psi-big4.org/target/draft_2006-08/ Draft pick of 460 BIG families (Aug 2006)]<br /> *[http://psi-big4.org/target/draft_2006-11/ Draft pick of 602 BIG families (Nov 2006)]<br /> *[http://psi-big4.org/target/small_mega_2007-03/ Selection of 3 small MEGA families (March 2007)]<br /> *[http://psi-big4.org/target/draft_2007-05/ First round draft pick of p-loop super MEGA (May 2007)]<br /> *[http://psi-big4.org/target/draft_2007-06/ Second round draft pick of p-loop super MEGA (June 2007)]<br /> *[http://psi-big4.org/target/draft_2007-06_gut/ First round META genome draft pick (June 2007)]<br /> *[http://psi-big4.org/target/small_mega_2007-06/ Selection of 4 small MEGA families (June 2007)]<br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ Draft selection of 4 mid size MEGA families (Dec 2007)<br>]<br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ ][http://psi-big4.org/target/super_mega_2007-12/3.40.50.720/ Draft pick of NAD(P)-binding Rossmann domain (Dec 2007)]<br /> *[http://psi-big4.org/target/super_mega_2007-12/3.20.20.70/ Draft pick of Aldolase Class I (Dec 2007)]<br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.150/ Draft pick of VP39 (Dec 2007)]<br /> *[http://psi-big4.org/target/draft_2008-05/ Draft pick of 1000 MEGA modeling families (250/center) (May 2008)]<br /> *[http://psi-big4.org/target/draft_2008-07/ Draft pick of 136 META HMM families (34/center) (July 2008)]<br /> *[http://psi-big4.org/target/draft_2008-07_mega/ Draft pick of 1000 MEGA modeling families (250/center) (July 2008)]</div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2611 Target selection 2009-12-01T16:56:37Z

<p>JohnEverett: </p> <hr /> <div>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families assigned by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the accademic community and 30%&nbsp;to its own biomedically oriented projects such as key proteins in Human cancer interaction<br>networks and bacterial lipoproteins. <br /> <br /> Throughout PSI-2, protein families proposed by the PSI&nbsp;BIG&nbsp;group have been selected by the PSI-2 large scale centers via a lottery system overseen by the <br>PSI&nbsp;BIG&nbsp;group.&nbsp; Members of protein families selected by the BIG&nbsp;group are studied by the large scale centers prior to family selection and each center proposes<br>families that they wish to pursue.&nbsp; The PSI&nbsp;BIG&nbsp;group resovles conflicts where more than one large scale center prposes the same protein family. <br /> <br /> Result of PSI-2 protein family drafts:<br /> <blockquote><br /> *[http://psi-big4.org/target/draft_2005-10/ Draft pick of 1369 Pfam families (Oct 2005)] <br /> *[http://psi-big4.org/target/draft_2006-04/ Draft pick of 397 BIG families (Apr 2006)] <br /> *[http://psi-big4.org/target/draft_2006-08/ Draft pick of 460 BIG families (Aug 2006)] <br /> *[http://psi-big4.org/target/draft_2006-11/ Draft pick of 602 BIG families (Nov 2006)] <br /> *[http://psi-big4.org/target/small_mega_2007-03/ Selection of 3 small MEGA families (March 2007)] <br /> *[http://psi-big4.org/target/draft_2007-05/ First round draft pick of p-loop super MEGA (May 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06/ Second round draft pick of p-loop super MEGA (June 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06_gut/ First round META genome draft pick (June 2007)] <br /> *[http://psi-big4.org/target/small_mega_2007-06/ Selection of 4 small MEGA families (June 2007)] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ Draft selection of 4 mid size MEGA families (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.720/ Draft pick of NAD(P)-binding Rossmann domain (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.20.20.70/ Draft pick of Aldolase Class I (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.150/ Draft pick of VP39 (Dec 2007)] <br /> *[http://psi-big4.org/target/draft_2008-05/ Draft pick of 1000 MEGA modeling families (250/center) (May 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07/ Draft pick of 136 META HMM families (34/center) (July 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07_mega/ Draft pick of 1000 MEGA modeling families (250/center) (July 2008)]<br /> </blockquote></div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2608 Target selection 2009-12-01T16:48:46Z

<p>JohnEverett: </p> <hr /> <div>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families assigned by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the accademic community and 30%&nbsp;to its own biomedically oriented projects such as key proteins in Human cancer interaction<br>networks and bacterial lipoproteins. <br /> <br /> <br /> <br /> Throughout PSI-2, protein families have been selected by thePSI-2 large scale centers via a lottery system overseen by the PSI&nbsp;BIG&nbsp;group.<br>Members of protein families selected by the BIG&nbsp;group are studied by the large scale centers and each center propose to work on<br>on particuliar protein families.&nbsp; The PSI&nbsp;BIG&nbsp;group resovles conflicts where more than one large scale center prposes the same protein family.<br /> <br /> <br> <br /> <blockquote><br /> *[http://psi-big4.org/target/draft_2005-10/ Draft pick of 1369 Pfam families (Oct 2005)] <br /> *[http://psi-big4.org/target/draft_2006-04/ Draft pick of 397 BIG families (Apr 2006)] <br /> *[http://psi-big4.org/target/draft_2006-08/ Draft pick of 460 BIG families (Aug 2006)] <br /> *[http://psi-big4.org/target/draft_2006-11/ Draft pick of 602 BIG families (Nov 2006)] <br /> *[http://psi-big4.org/target/small_mega_2007-03/ Selection of 3 small MEGA families (March 2007)] <br /> *[http://psi-big4.org/target/draft_2007-05/ First round draft pick of p-loop super MEGA (May 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06/ Second round draft pick of p-loop super MEGA (June 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06_gut/ First round META genome draft pick (June 2007)] <br /> *[http://psi-big4.org/target/small_mega_2007-06/ Selection of 4 small MEGA families (June 2007)] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ Draft selection of 4 mid size MEGA families (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.720/ Draft pick of NAD(P)-binding Rossmann domain (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.20.20.70/ Draft pick of Aldolase Class I (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.150/ Draft pick of VP39 (Dec 2007)] <br /> *[http://psi-big4.org/target/draft_2008-05/ Draft pick of 1000 MEGA modeling families (250/center) (May 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07/ Draft pick of 136 META HMM families (34/center) (July 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07_mega/ Draft pick of 1000 MEGA modeling families (250/center) (July 2008)]<br /> </blockquote></div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2604 Target selection 2009-12-01T16:44:41Z

<p>JohnEverett: </p> <hr /> <div>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families assigned by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the accademic community and 30%&nbsp;to its own biomedically oriented projects such as key proteins in Human cancer interaction<br>networks and bacterial lipoproteins. <br /> <br /> <br> <br /> <blockquote><br /> *[http://psi-big4.org/target/draft_2005-10/ Draft pick of 1369 Pfam families (Oct 2005)] <br /> *[http://psi-big4.org/target/draft_2006-04/ Draft pick of 397 BIG families (Apr 2006)] <br /> *[http://psi-big4.org/target/draft_2006-08/ Draft pick of 460 BIG families (Aug 2006)] <br /> *[http://psi-big4.org/target/draft_2006-11/ Draft pick of 602 BIG families (Nov 2006)] <br /> *[http://psi-big4.org/target/small_mega_2007-03/ Selection of 3 small MEGA families (March 2007)] <br /> *[http://psi-big4.org/target/draft_2007-05/ First round draft pick of p-loop super MEGA (May 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06/ Second round draft pick of p-loop super MEGA (June 2007)] <br /> *[http://psi-big4.org/target/draft_2007-06_gut/ First round META genome draft pick (June 2007)] <br /> *[http://psi-big4.org/target/small_mega_2007-06/ Selection of 4 small MEGA families (June 2007)] <br /> *[http://psi-big4.org/target/midsize_mega_2007-12/ Draft selection of 4 mid size MEGA families (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.720/ Draft pick of NAD(P)-binding Rossmann domain (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.20.20.70/ Draft pick of Aldolase Class I (Dec 2007)] <br /> *[http://psi-big4.org/target/super_mega_2007-12/3.40.50.150/ Draft pick of VP39 (Dec 2007)] <br /> *[http://psi-big4.org/target/draft_2008-05/ Draft pick of 1000 MEGA modeling families (250/center) (May 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07/ Draft pick of 136 META HMM families (34/center) (July 2008)] <br /> *[http://psi-big4.org/target/draft_2008-07_mega/ Draft pick of 1000 MEGA modeling families (250/center) (July 2008)]<br /> </blockquote></div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2602 Target selection 2009-12-01T16:43:05Z

<p>JohnEverett: </p> <hr /> <div>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families assigned by the [http://psi-big4.org PSI&nbsp;BIG&nbsp;group], <br>30% to targets nominated by the accademic community and 30%&nbsp;to its own biomedically oriented projects such as key proteins in Human cancer interaction<br>networks and bacterial lipoproteins.</div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2601 Target selection 2009-12-01T16:41:23Z

<p>JohnEverett: </p> <hr /> <div>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination of targeted families assigned by the PSI&nbsp;BIG&nbsp;group, <br>30% to targets nominated by the accademic community and 30%&nbsp;to its own biomedically oriented projects such as key proteins in Human cancer interaction<br>networks and bacterial lipoproteins.</div>

JohnEverett https://nesgwiki.chem.buffalo.edu/index.php?title=Target_selection&diff=2600 Target selection 2009-12-01T16:41:02Z

<p>JohnEverett: </p> <hr /> <div>As part of the NIH funded PSI-2 project, the NESG dedicates 70%&nbsp;of its resources to the determination<br>of targeted families assigned by the PSI&nbsp;BIG&nbsp;group, 30% to targets nominated by the accademic community<br>and 30%&nbsp;to its own biomedically oriented projects such as key proteins in Human cancer interaction networks<br>and bacterial lipoproteins.</div>

JohnEverett