User contributions for Admin

13 October 2009

• 15:2215:22, 13 October 2009 diff hist −13‎ Mass Spectrometry ‎No edit summary
• 15:2015:20, 13 October 2009 diff hist −65‎ Mass Spectrometry ‎No edit summary
• 15:1915:19, 13 October 2009 diff hist −53‎ Mass Spectrometry ‎No edit summary
• 15:0815:08, 13 October 2009 diff hist −80‎ NESG:OligomerizationStatus ‎No edit summary current

12 October 2009

• 16:5016:50, 12 October 2009 diff hist −11‎ NESG:OligomerizationStatus ‎No edit summary
• 16:5016:50, 12 October 2009 diff hist +25‎ NESG:OligomerizationStatus ‎No edit summary
• 16:4716:47, 12 October 2009 diff hist +8‎ NESG:OligomerizationStatus ‎No edit summary
• 16:4616:46, 12 October 2009 diff hist −7‎ NESG:OligomerizationStatus ‎No edit summary
• 16:4516:45, 12 October 2009 diff hist −3‎ NESG:OligomerizationStatus ‎No edit summary
• 16:4316:43, 12 October 2009 diff hist +9‎ NESG:SampleCheck ‎No edit summary current
• 16:4116:41, 12 October 2009 diff hist −13‎ NESG:OligomerizationStatus ‎No edit summary
• 16:4116:41, 12 October 2009 diff hist −9‎ NESG:OligomerizationStatus ‎No edit summary
• 16:4116:41, 12 October 2009 diff hist −2‎ NESG:OligomerizationStatus ‎No edit summary
• 16:3916:39, 12 October 2009 diff hist +8‎ NESG:OligomerizationStatus ‎No edit summary
• 16:3816:38, 12 October 2009 diff hist −12‎ NESG:SampleCheck ‎No edit summary
• 16:3516:35, 12 October 2009 diff hist +24‎ NESG:SampleCheck ‎No edit summary
• 16:3116:31, 12 October 2009 diff hist +4‎ NESG:SampleCheck ‎No edit summary
• 16:3016:30, 12 October 2009 diff hist +14‎ NESG:SampleCheck ‎No edit summary
• 15:5715:57, 12 October 2009 diff hist +12‎ NESG:Acquiring an NMR Sample ‎No edit summary
• 15:5315:53, 12 October 2009 diff hist −27‎ NESG:Acquiring an NMR Sample ‎No edit summary
• 15:5115:51, 12 October 2009 diff hist 0‎ N File:Snapshot1.jpg ‎No edit summary current
• 15:4215:42, 12 October 2009 diff hist −26‎ NESG:Acquiring an NMR Sample ‎No edit summary
• 15:4115:41, 12 October 2009 diff hist +3‎ NESG:Acquiring an NMR Sample ‎No edit summary
• 15:3915:39, 12 October 2009 diff hist −101‎ NESG:Acquiring an NMR Sample ‎No edit summary
• 15:3215:32, 12 October 2009 diff hist −9‎ NESG:Acquiring an NMR Sample ‎No edit summary
• 15:2915:29, 12 October 2009 diff hist −5‎ NESG:Acquiring an NMR Sample ‎No edit summary
• 15:2115:21, 12 October 2009 diff hist +3‎ NESG:Acquiring an NMR Sample ‎No edit summary
• 15:2015:20, 12 October 2009 diff hist −30‎ NESG:Acquiring an NMR Sample ‎No edit summary
• 14:5214:52, 12 October 2009 diff hist −37‎ NESG:MasterRecipe/HTPFlowChart ‎No edit summary
• 14:5114:51, 12 October 2009 diff hist −8‎ NESG:MasterRecipe/HTPFlowChart ‎No edit summary
• 14:5014:50, 12 October 2009 diff hist −5‎ NESG:MasterRecipe/HTPFlowChart ‎No edit summary
• 14:4914:49, 12 October 2009 diff hist −195‎ NESG:MasterRecipe/HTPFlowChart ‎No edit summary
• 14:4914:49, 12 October 2009 diff hist +194‎ NESG:MasterRecipe/HTPFlowChart ‎No edit summary
• 14:4814:48, 12 October 2009 diff hist −194‎ NESG:MasterRecipe/HTPFlowChart ‎No edit summary
• 14:4814:48, 12 October 2009 diff hist +2,094‎ N NESG:MasterRecipe/HTPFlowChart ‎ Created page with '== '''NESG High Throughput NMR Structure Determination Flow Chart''' == <h2> <b> {| border="1" |- | <b>Steps<br /></b> || <b><br /></b> || Approaches<br /> || <b>Program…'
• 14:4614:46, 12 October 2009 diff hist +4,826‎ N NESG:HistidinepKaDetermination ‎ Created page with '== '''Histidine pKa Determination''' == The imidazole side chain of histidine exhibits a relatively neutral pKa. Consequently, Nature employs the versatile histidine residue f…'
• 14:1814:18, 12 October 2009 diff hist +19,516‎ N RDC-Assisted Dimer Structure Determination ‎ Created page with ' <strong>Introduction</strong><br /><br />Protein homo-oligomers occur in nature frequently and some oligomerization processes can influence biological processes significantly. …'
• 14:1614:16, 12 October 2009 diff hist +3,302‎ N NESG:Identification and using cis Prolines in structure calculation ‎ Created page with '== '''Identification of cis amide bonds in prolines''' == The peptide bond can exist in two forms: ''cis'' or ''trans''. The corresponding dihedral angle "CA-C'-N(i+1)-CA(i+1)" …' current
• 14:1314:13, 12 October 2009 diff hist +19,740‎ N Structure Refinement Using CNS Energy Minimization With Explicit Water ‎ Created page with '== '''Structure Refinement Using CNS Energy Minimization With Explicit Water''' == The final structure from CYANA should be refined using CNS energy minimization with explicit w…'
• 14:0814:08, 12 October 2009 diff hist +3,071‎ Nm NESG:ApplyingSSA ‎ Created page with '== '''CYANA macros for stereospecific assignments''' == Stereospecific assignments are typically applied as separate CYANA macros. They contain two main commands: <tt>atom swap<…' current
• 14:0714:07, 12 October 2009 diff hist +5,976‎ N GLOMSA ‎ Created page with '== '''SSA with GLOMSA (GLObal Method for Stereospecific Assignment) Module''' == === '''Overview''' === {| border="1" |- * GLOMSA is performed with the preliminary conformers a…'
• 14:0514:05, 12 October 2009 diff hist +2,398‎ N NESG:RefinementWithRPF ‎ Created page with '== '''Refinement by Using RPF Violations Mapped on to the Structure''' == Since RPF scores can be used as a quality control in iterative cycle analysis of protein structure det…' current
• 14:0414:04, 12 October 2009 diff hist +2,914‎ N Manual Structure Calculation Using CYANA ‎ Created page with '== Manual structure calculation with CYANA 2.1 == Manual structure calculation is performed similar to the automated calculation. # Create a new work…'
• 14:0314:03, 12 October 2009 diff hist +3,245‎ N NESG:ManualNOEAssignment ‎ Created page with '== '''Manual Assignment of New NOEs''' == There are several methods can help manually assigned more NOE peaks and structure refinement: ## Check transpose peak in XEASY ## Check …' current
• 14:0214:02, 12 October 2009 diff hist +4,101‎ N NESG:OptimizingNOECalibration ‎ Created page with '== '''Optimizing Calibration with Calibration Plots in CALIBA''' == An overview of basic NOE calibration has been given earlier. Here we describe ho…' current
• 14:0114:01, 12 October 2009 diff hist +2,663‎ N Validation of Consensus Run ‎ Created page with '== '''Validation of Consensus Run''' == === '''Verification of Consensus Assignments''' === # Create a working subdirectory, for example, <tt>cyana21/calc2</tt>. # Copy consens…'
• 13:5913:59, 12 October 2009 diff hist +10,219‎ N Finding Consensus NOE Assignments ‎ Created page with '== '''Find Consensus NOE Assignment''' == By comparing the results from the programs CYANA and AutoStructure, identical NOE assignment are found and are regarded as correct NOE.…'
• 13:5813:58, 12 October 2009 diff hist +11,255‎ N NESG:AutoStructureRun ‎ Created page with '== '''AutoStructure Run''' == Before going to the AutoStructure run for automatic structure calculation, please check: * [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autostructu…'
• 13:5713:57, 12 October 2009 diff hist +16,249‎ N Automated NOESY Assignment Using CYANA ‎ Created page with '== '''CYANA Run''' == Unfortunately, there is no comprehensive CYANA manual. Many features can be found in the original DYANA manual. For a summary of features consult the CYANA…'
• 13:5513:55, 12 October 2009 diff hist +2,766‎ N Overview of Consensus Runs ‎ Created page with '== '''Overview of Consensus Runs''' == AutoStructure and CYANA 2.1 are used in parallel to run automatic structure calculations. Identical NOE assignments from both programs (''…'
• 13:5313:53, 12 October 2009 diff hist +10,685‎ N FOUND ‎ Created page with '== '''FOUND(HABAS)''' == === '''Introduction''' === '''FOUND''' performs systematic local conformation analysis by exhaustive grid searches for arbitrary contiguous fragments …'
• 13:5213:52, 12 October 2009 diff hist +12,901‎ N NESG:NOECalibrationCYANA ‎ Created page with '== '''NOE Calibration: Finding calibration Parameters for Distance Constraints''' == NOE calibration converts NOESY cross-peak intensities into upper distance limits. A certain …' current
• 13:5113:51, 12 October 2009 diff hist +3,581‎ N SSAFromFractional13CLabeledSample ‎ Created page with '== '''Stereospecific assignments with a 13C Fractionally Labeled Sample''' == Isopropyl groups of Val and Leu can be sterospecifically assigned with the help of a 5-10% fraction…'
• 13:4913:49, 12 October 2009 diff hist +4,364‎ N TALOS ‎ Created page with '== '''Finding Dihedral Angle Constraints with TALOS''' == TALOS (Torsion Angle Likelihood Obtained from Shift and sequence similarity) is a database system for empirical predict…'
• 13:4713:47, 12 October 2009 diff hist +1,188‎ N NESG:CARAExportingXeasyFiles ‎ Created page with '== '''Exporting PeakLists, AtomLists and Sequence from CARA''' == === '''Sequence''' === You can export an XEASY-format sequence file by right-clicking on your project tab and …' current
• 13:4613:46, 12 October 2009 diff hist +1,769‎ N NESG:CYANAInitFile ‎ Created page with '== '''Creating an init.cya file''' == The init.cya is a local initialization file, which is read when cyana starts. It should be located in the directory where CYANA is run. In …' current

9 October 2009

• 17:5717:57, 9 October 2009 diff hist +8,124‎ N NESG:CARAGeneratingNOESYPeaklists ‎ Created page with ' == '''Generating NOESY Peaklists in CARA''' == === '''Simulating Blank NOESY Peaklists (Recommended)''' === It is recommended to start with a blank peaklist. Note that in t…' current
• 17:5517:55, 9 October 2009 diff hist +5,705‎ N NESG:GeneratingNOESYPeaklists ‎ Created page with ' == '''Generating NOESY Initial Peaklist with XEASY/UBNMR''' == === '''Simulating NOESY Peaklists for XEASY''' === Before NOESY analysis, initial NOESY peak lists are simula…' current
• 17:5417:54, 9 October 2009 diff hist +1,785‎ N NESG:OverviewStructureCalculation ‎ Created page with ' == '''Overview of Structure Calculation and Refinement Protocol''' == === Outline === # Simulate initial NOE peaklists (intra and short connectivities), pick additional pea…' current
• 17:5317:53, 9 October 2009 diff hist +16‎ NESG:CSISecondaryStructurePrediction ‎No edit summary current
• 17:5317:53, 9 October 2009 diff hist +1,400‎ N NESG:CSISecondaryStructurePrediction ‎ Created page with ' == '''Secondary Structure Element Prediction Using CSI''' == You can predict secondary structure from HA, CA, CB and CO chemical shifts by using CSI. See the [http://www.bionm…'
• 17:5117:51, 9 October 2009 diff hist +1,518‎ N NESG:AssignmentValidation ‎ Created page with ' == '''Assignment Validation''' == === '''AVS''' === Once the assignment results were obtained from, it is required to validate the assignments. AutoAssign provides Assignmen…' current
• 17:5017:50, 9 October 2009 diff hist +3,451‎ N Amide Side Chain Assignment with CARA ‎ Created page with ' == '''Amide Side-chain Resonance Assignment''' == You will normally need to have 3 windows open at the same time: # Open aliphatic 2D [13C, 1H]-HSQC with '''Open PolyScope'''…'
• 17:4917:49, 9 October 2009 diff hist +12,041‎ N Aromatic Side Chain Assignment with CARA ‎ Created page with ' == '''Aromatic Side-chain Resonance Assignment''' == Overall, aromatic side-chain assignment is very similar to aliphatic side-chain assignment, only one uses aromatic (H)CCH-…'
• 17:4817:48, 9 October 2009 diff hist +36,749‎ N Resonance Assignment/CARA/Aliphatic side-chain assignment ‎ Created page with ' == '''Aliphatic Side-chain Resonance Assignment''' == === '''Introduction''' === For a short overview of heteronuclear side-chain assignment see this page: http://www.cara.…'
• 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…'