User contributions for Admin

9 October 2009

• 17:4617:46, 9 October 2009 diff hist +3,413‎ N Resonance Assignment/CARA/Backbone assignment GFT ‎ Created page with '=== '''HA And HB Assignment in (4,3)D HABCAB(CO)NHN with CARA''' === # Run '''GFT_CreateHABProjSpins''' Lua script to create GFT spins like <nop>CApHA-1 and <nop>CBpHB-1. Known…'
• 17:4517:45, 9 October 2009 diff hist +5,118‎ N Resonance Assignment/CARA/Backbone assignment ‎ Created page with '== '''Backbone Assignment with CARA''' == === '''Picking Spins in (4,3)D GFT HNNCABCA and CABCA(CO)NHN Spectra''' === Open (4,3)D GFT HNNCABCA and CABCA(CO)NHN in SynchroScope …'
• 17:4417:44, 9 October 2009 diff hist +1,480‎ N Spin System Identification with CARA ‎ Created page with '== '''Spin System Identification with CARA''' == Spin system identification in 2D [15N,1H]-HSQC and 3D HNCO # Open a repositiry or create one if it does not exist (see the CARA…'
• 17:4317:43, 9 October 2009 diff hist +6,599‎ N Side chain assignment with CN-NOESY in XEASY ‎ Created page with '== '''Side Chain Assignments Using Simultaneous 15N,13C-resolved(1H,1H)NOESY''' == One can go to the simultaneous 15N,13C-resolved(1H,1H)NOESY directly other than HCCH to finish…'
• 17:3617:36, 9 October 2009 diff hist +1,984‎ N Met methyl assignment with NOESY ‎ Created page with '== '''Met Methyl Resonance Assignment''' == Usually, the Met methyl resonance assignment can be obtained from NOESY, however, in a different manner as described above. The Met m…'
• 17:3417:34, 9 October 2009 diff hist +6,006‎ N Amide Side Chain assignment with NOESY ‎ Created page with '== '''Amide Side-chain Resonance Assignment Using The Simultaneous 15N, 13C-resolved (1H,1H) NOESY''' == The amide side-chain resonance assignment here means the assignment of a…'
• 17:3317:33, 9 October 2009 diff hist −456‎ Aromatic side chain assignment with Aro-HCCH-COSY in XEASY ‎No edit summary
• 17:3217:32, 9 October 2009 diff hist +3,281‎ N Aromatic side chain assignment with Aro-HCCH-COSY in XEASY ‎ Created page with '<br><br>== '''Aromatic Side-chain Resonance Assignment Using the Aromatic HCCHCOSY Spectrum'''  ==<br><br><br>Aromatic (4,3)D HCCH shows signals for aromatic H-C-C-H moeties…'
• 17:3117:31, 9 October 2009 diff hist +13,200‎ N Side chain assignment with aliphatic (4,3)D HCCH-COSY in XEASY ‎ Created page with ' == '''Aliphatic Side-chain Resonance Assignment Using the Aliphatic HCCHCOSY Spectrum''' == The sequence specific 15N /1HN /13CAB resonance assignments obtained as described …'
• 16:3816:38, 9 October 2009 diff hist +4,498‎ N HA and HB Assignment with GFT in XEASY ‎ Created page with '== '''HA And HB Assignments with XEASY/UBNMR''' == HA and HB assignments provide the bridge from BackboneAssignment to the complete [[NESG:SideChainA…'
• 16:3716:37, 9 October 2009 diff hist +16,187‎ N XEASY Backbone Assignment ‎ Created page with '== '''Backbone Assignment with XEASY/UBNMR''' == Sequential backbone and 13CB resonance assignment is associated with mapping of SRDs identified in spin system identification on…'
• 16:3716:37, 9 October 2009 diff hist +5,829‎ N XEASY Spin system identification ‎ Created page with ' == '''Spin System Identification''' == 2D [15N,1H]-HSQC provide pairs of correlated amide 15N / 1HN chemical shifts. They seed '''spin systems''' - spins of individual r…'
• 16:3416:34, 9 October 2009 diff hist +1,120‎ N NESG:OverviewOfAssignmentProtocol ‎ Created page with '== '''Overview of Assignment Protocol''' == The current assignment protocol is developed with mainly using the program XEASY for spectral analsis, which might shift to using CAR…' current
• 15:3915:39, 9 October 2009 diff hist +1‎ Homodimer Structure Calculation Using CYANA ‎No edit summary
• 15:3815:38, 9 October 2009 diff hist −1‎ Homodimer Structure Calculation Using CYANA ‎No edit summary
• 15:3515:35, 9 October 2009 diff hist +2‎ Homodimer Structure Calculation Using CYANA ‎No edit summary
• 15:3415:34, 9 October 2009 diff hist +11‎ Homodimer Structure Calculation Using CYANA ‎No edit summary
• 15:3315:33, 9 October 2009 diff hist +34‎ Homodimer Structure Calculation Using CYANA ‎No edit summary
• 15:3015:30, 9 October 2009 diff hist +2,446‎ Homodimer Structure Calculation Using CYANA ‎No edit summary
• 14:5714:57, 9 October 2009 diff hist +2,273‎ N Structure Calculation Using CS-Rosetta ‎ Created page with '== '''Structure Calculation with CS-Rosetta''' == === '''Original Documentation''' === http://spin.niddk.nih.gov/bax/software/CSROSETTA/index.html === '''Random Coil Index Pre…'
• 14:5614:56, 9 October 2009 diff hist +819‎ N NESG:PfamProteinFamilies ‎ Created page with '== '''PfamProteinFamilies''' == PfamProteinFamilies (http://www.sanger.ac.uk/Software/PfamProteinFamilies/) is a large collection of multiple sequence alignments and hidden Mark…'
• 14:4814:48, 9 October 2009 diff hist +27,639‎ N NESG:RDCScreening ‎ Created page with '-- Main.SonalBansal - 07 Sep 2007 -- Main.DavidParish - 09 Nov 2007 == RDC Screening and Structure Refinement == Residual Dipolar Couplings (RDCs) originate from the anisotrop…' current
• 14:4514:45, 9 October 2009 diff hist +2,279‎ N Rosetta High Resolution Protein Structure Refinement Protocol ‎ Created page with '== '''Rosetta High Resolution Protein Structure Refinement Protocol''' == Before running Rosetta, please make directory with: * rosetta_database (directory) ** paths.txt ** 1…'
• 14:4314:43, 9 October 2009 diff hist +2,459‎ N Homodimer Structure Calculation Using CYANA ‎ Created page with '== '''Dimer Structure Calculation by CYANA''' == CYANA2.1 can handle handle structure calculation: === '''Symmetric Dimers''' === Two new types of restraints have been introd…'
• 14:4314:43, 9 October 2009 diff hist +147‎ N NESG:StructureDimer ‎ Created page with '== '''Structure Calculation for Dimer''' == === Dimer structure calculation by CYANA === -- Main.GaohuaLiu - 09 Nov 2007' current
• 14:4114:41, 9 October 2009 diff hist +2‎ NESG:PsiBLAST ‎No edit summary current
• 14:4014:40, 9 October 2009 diff hist +2,144‎ N NESG:PsiBLAST ‎ Created page with '==*PSIBLAST* == PSIBLAST iteratively searches one or more protein databases for sequences similar to one or more protein query sequences. PSIBLAST is similar to BLAST except tha…'
• 14:3814:38, 9 October 2009 diff hist +3,913‎ N NESG:StructureSimilaritySearch ‎ Created page with '== '''Structure Similarity Search''' == === '''DALI''' === The [http://www.ebi.ac.uk/dali/ DALI] server is a network service for comparing protein structures in 3D. One submits t…'
• 14:3714:37, 9 October 2009 diff hist +1,518‎ N NESG:BioInformaticsResources ‎ Created page with '== '''Resources for Bioinformatics and Functional Annotation''' == === '''Meta Servers''' === ==== '''Mark-Us (B. Honig, Columbia)''' ==== [http://wiki.c2b2.columbia.edu/honig…'
• 14:3614:36, 9 October 2009 diff hist +12,827‎ N PDB and BMRB Deposition ‎ Created page with '== '''BMRB and PDB Structure Depositions''' == '''NESG SOP For NMR PDB/BMRB Structure Depositions (Dec, 2006)''' ''Note: Truncated coordinates: Researchers used to deposit NMR …'
• 14:3414:34, 9 October 2009 diff hist +11,488‎ N NESG:AutoStructureRPFScores ‎ Created page with '== '''RPF Scores From AutoStructure: Protein NMR structure quality assessment tool''' == This section is taken from the SOP of AutoStructure, please check: * [http://www-nmr.cab…' current
• 14:3314:33, 9 October 2009 diff hist +2,917‎ N NESG:RunningProcheckNMR ‎ Created page with '== '''RunningProcheckNMR''' == [http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html Procheck] checks the stereochemical quality of a protein structure, producing a number…' current
• 14:3114:31, 9 October 2009 diff hist +2,600‎ N PSVS ‎ Created page with '== '''Running the PSVS Server''' == [http://www-nmr.cabm.rutgers.edu/PSVS/ PSVS] (protein structure validation server) systematically evaluates the quality of protein structures…'

8 October 2009

• 15:4815:48, 8 October 2009 diff hist +571‎ N NESG:ProFunc ‎ Created page with '== '''ProFunc''' == [http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/ ProFunc] is a server offered by the [http://www.ebi.ac.uk/Thornton/ Thornton Group] at EBI. It was deve…' current
• 15:4615:46, 8 October 2009 diff hist +734‎ N NESG:NMRDataArchiving ‎ Created page with '== '''NMR Data Archiving''' == === '''Routine Data Backup''' === Although the Main.HTP server backup data daily, it is required to routinely backup data about project progress. O…'
• 15:4515:45, 8 October 2009 diff hist +1,547‎ N NESG:PeakDetectionYield ‎ Created page with '== '''Determination of Peak Detection Yield''' == It is required to determine the peak detection yield of a NMR spectrum as earlier as possible. Determination of approximate pea…'
• 15:4415:44, 8 October 2009 diff hist +2,030‎ N NESG:FormatConversion ‎ Created page with '== '''NMR Spectra Format Conversion''' == === '''Conversion from Buffalo.NMRPipe Format to XEASY Format''' === After optimizing phase, macro <tt>doit.com</tt> is used to run lin…' current
• 15:4315:43, 8 October 2009 diff hist +3,136‎ N NESG:AGNuS ‎ Created page with '==*Autoproc/AGNuS* == [http://www-nmr.cabm.rutgers.edu/software/autoproc.htm Autoproc/AGNuS] is a suite of programs for the automatic generation of scripts for multidimensional p…' current
• 15:4115:41, 8 October 2009 diff hist +11,024‎ N NESG:BuffaloNMRPipeFT ‎ Created page with '== '''Data Processing Protocol''' == In the <tt>process</tt> directory, go to the directory of the experiment you would like to process and check the README file for instru…' current
• 15:4015:40, 8 October 2009 diff hist +1,660‎ N NESG:TransferDataFromNMRSpectrometer ‎ Created page with '== '''Transfer Data From NMR Spectrometer''' == Go to the <tt>acq</tt> directory under the target directory. Check README for instructions: * This directory will contain ONLY yo…' current
• 15:3915:39, 8 October 2009 diff hist +1,211‎ N NESG:AutomaticGenerationOfProjectDirectoryTree ‎ Created page with '== '''Automatic Generation of Project Directory Tree''' == A set of multi-dimensional heteronuclear GFT NMR experiments (see [http://pubs.acs.org/cgi-bin/searchRedirect.cgi/jacs…' current
• 15:3815:38, 8 October 2009 diff hist +544‎ N NESG:BuffaloProcessProctocol ‎ Created page with '== '''Buffalo's Process Proctocol''' == The current Buffalo processing protocols described here have been developed for NMRpipe with help of Perl Scrips developed by Dr. David P…' current
• 15:3715:37, 8 October 2009 diff hist +835‎ N NESG:DataProcessing ‎ Created page with '== '''Data Processing Overview''' == The current data processing protocols (by using Buffalo scripts or AGNuS) described here are similar as both protocols were designed around …' current
• 15:3515:35, 8 October 2009 diff hist +3,695‎ N NESG:ExperimentSpecificNMRParameters ‎ Created page with '== '''Experiment-specific NMR Parameters''' == It would be very helpful to start with previously optimized parameter set. * Parameters for 2D Experiments for proteins ** 2D 15N…' current
• 15:3415:34, 8 October 2009 diff hist +1,043‎ N NESG:OtherNMRParametersOptimization ‎ Created page with '== Other Parameters == === Amplifier Compression === NMR amplifiers normally exhibit non-linear response at the peak power used for high pulses. This non-linearity has to be ta…' current
• 15:3315:33, 8 October 2009 diff hist +8,840‎ N NESG:SettingUpMultidimensionalNMRExperiments ‎ Created page with '= '''Setting Up Multidimensional NMR Experiments''' = It is recommended to collect different NMR data sets depending on the behavior of the protein, and collect the NOESY spectr…' current
• 15:3115:31, 8 October 2009 diff hist +1,387‎ N Long-range 15N-1H correlation experiments for histidine rings ‎ Created page with '== 2D [15N, 1H] long-range HSQC for His rings == === Varian === This pulse sequence correlates aromatic H-C protons of His with ring nitrogens. Use the <tt>rna_WGgNhsqclr</tt>…'
• 15:3015:30, 8 October 2009 diff hist +628‎ N NESG:HCCHTocsY ‎ Created page with '== Aliphatic 3D (H)CCH-TOCSY == Slightly modified version of the <tt>cch_tocsyA.c</tt> in BioPack. * Corrected small uncompensated initial evolution in 13C t1 dimension * Chang…' current
• 15:2915:29, 8 October 2009 diff hist +1,893‎ N NESG:43DGFTHCCHCosYali ‎ Created page with '== (4,3)D GFT HCCH-COSY Aliphatic == Written by Youlin Xia and H. Atreya. Modified by Main.AlexEletski Requires pre-installed BioPack. [[NESG:%PUBURLPATH%/Buffalo/43DGFTHCCHCo…' current
• 15:2615:26, 8 October 2009 diff hist +2,145‎ N NESG:43DGFTHabCabconhn ‎ Created page with '== (4,3)D GFT HABCAB(CO)NHN == Written by Youlin Xia and H. Atreya. Modified by Main.AlexEletski Requires pre-installed BioPack. [[NESG:%PUBURLPATH%/Buffalo/43DGFTHabCabconhn/…' current