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MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

I. W. Davis, A. Leaver-Fay, V. B. Chen, J. N. Block, G. J. Kapral, X. Wang, L. W. Murray, W. B. Arendall, J. Snoeyink, J. S. Richardson, D. C. Richardson
2007 Nucleic Acids Research  
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes.  ...  It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedralangle diagnostics, and it can calculate and display the H-bond and van der Waals contacts  ...  ACKNOWLEDGEMENTS Maintenance and development of MolProbity is supported by NIH grant GM-073919. IWD acknowledges a Howard Hughes predoctoral fellowship, and JNB an NIH NRSA fellowship.  ... 
doi:10.1093/nar/gkm216 pmid:17452350 pmcid:PMC1933162 fatcat:zh5us23wa5d6hpkqm6bvjmgaz4

MolProbity: all-atom structure validation for macromolecular crystallography

Vincent B. Chen, W. Bryan Arendall, Jeffrey J. Headd, Daniel A. Keedy, Robert M. Immormino, Gary J. Kapral, Laura W. Murray, Jane S. Richardson, David C. Richardson
2009 Acta Crystallographica Section D: Biological Crystallography  
MolProbityis a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids.  ...  X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple  ...  Ian Davis is the initial developer of the MolProbity site, Xueyi Wang and Jack Snoeyink programmed RNABC, Jeremy Block developed MolProbity functions for NMR and the PHENIX development team at LBL were  ... 
doi:10.1107/s0907444909042073 pmid:20057044 pmcid:PMC2803126 fatcat:rlfdwhmc2rfyvdgzbtuwshkl7a

MolProbity: all-atom structure validation for macromolecular crystallography [chapter]

V. B. Chen, W. B. Arendall, J. J. Headd, D. A. Keedy, R. M. Immormino, G. J. Kapral, L. W. Murray, J. S. Richardson, D. C. Richardson
2012 International Tables for Crystallography  
Ian Davis is the initial developer of the MolProbity site, Xueyi Wang and Jack Snoeyink programmed RNABC, Jeremy Block developed MolProbity functions for NMR and the PHENIX development team at LBL were  ...  very helpful with AUTOFIX and with integration of MolProbity functions.  ...  MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids.  ... 
doi:10.1107/97809553602060000884 fatcat:53l2v6kyffcgdppsua5pn2qsby

MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes

I. W. Davis, L. W. Murray, J. S. Richardson, D. C. Richardson
2004 Nucleic Acids Research  
MOLPROBITY is a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes.  ...  It provides detailed all-atom contact analysis of any steric problems within the molecules and can calculate and display the H-bond and van der Waals contacts in the interfaces between components.  ...  INTRODUCTION Experimental structure determination has rather different strengths and weaknesses for nucleic acids than for the protein case, where most validation methods were developed.  ... 
doi:10.1093/nar/gkh398 pmid:15215462 pmcid:PMC441536 fatcat:6m5y5ii4lvcpjcnu7ktilv7lxm

MolProbity: More and better reference data for improved all-atom structure validation

Christopher J. Williams, Jeffrey J. Headd, Nigel W. Moriarty, Michael G. Prisant, Lizbeth L. Videau, Lindsay N. Deis, Vishal Verma, Daniel A. Keedy, Bradley J. Hintze, Vincent B. Chen, Swati Jain, Steven M. Lewis (+6 others)
2017 Protein Science  
We thank Laura Murray for compiling RNA05 and starting RNA11, Ralf Grosse-Kunstleve for the hybrid36 format and its converters, Richard Gildea for scripts in  ...  Acknowledgements Funding: National Institutes of health grants R01-GM073919 to DCR, P01-GM063210 subcontract to JSR, R01-GM088674 to JSR, R01-GM073930 to DCR and its ARRA supplement, and DUMC bridge funding  ...  Introduction MolProbity is a widely used system of model validation for protein and nucleic acid structures, accessed at http://molprobity.biochem.duke.edu.  ... 
doi:10.1002/pro.3330 pmid:29067766 fatcat:3u55axsr2zeirl2kcoxgseu4za

CaBLAM for CryoEM Chiropraxis, UnDowser to Rethink "Waters", and NGL Viewer to Recapture Online 3D Graphics in MolProbity Validation [article]

Michael G Prisant, Christopher J Williams, Vincent B Chen, Jane Shelby Richardson, David C Richardson
2019 bioRxiv   pre-print
The MolProbity web service provides macromolecular model validation to help correct local errors, for the structural biology community worldwide.  ...  CaBLAM, our first new tool designed for this regime, was described in the previous Tools issue, and here we demonstrate its effectiveness in diagnosing local errors even when other validation outliers  ...  favorable sites where they H-bond to protein, nucleic acid, or ligands.  ... 
doi:10.1101/795161 fatcat:hjb67ejegjdo3ixkdowcy2adje

Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place

Jeffrey J. Headd, Robert M. Immormino, Daniel A. Keedy, Paul Emsley, David C. Richardson, Jane S. Richardson
2008 Journal of Structural and Functional Genomics  
The MolProbity web site is effective at diagnosing such errors, and can perform reliable automated correction of a few special cases such as 180°flips of Asn or Gln sidechain amides, using all-atom contacts  ...  A fully automated method called "Autofix" identifies such errors for Leu, Val, Thr, and Arg and corrects over one third of them, using MolProbity validation criteria and Coot realspace refinement of rotamers  ...  statistics of MolProbity, Gary Kapral for help with analyzing the 1YHQ ribosome structure, and Lizbeth Videau for initial conversations that inspired this work.  ... 
doi:10.1007/s10969-008-9045-8 pmid:19002604 pmcid:PMC2704614 fatcat:mytn5pbpvjh3bnnt4suzhar54u

QRNAS: software tool for refinement of nucleic acid structures

Juliusz Stasiewicz, Sunandan Mukherjee, Chandran Nithin, Janusz M. Bujnicki
2019 BMC Structural Biology  
To obtain a high-quality model, the preliminary RNA structural model needs to be refined, taking into account atomic interactions.  ...  Computational models of RNA 3D structure often present various inaccuracies caused by simplifications used in structure prediction methods, such as template-based modeling or coarse-grained simulations  ...  Acknowledgments We thank members of the Bujnicki lab, in particular Grzegorz Łach, Grzegorz Chojnowski, Dorota Niedziałek, Adriana Żyła, Filip Stefaniak, Pritha Ghosh, and Almudena Ponce Salvatierra for  ... 
doi:10.1186/s12900-019-0103-1 pmid:30898165 pmcid:PMC6429776 fatcat:qrky7vdlzzfsrgddd5enyypcuq

Stereochemistry and Validation of Macromolecular Structures [chapter]

Alexander Wlodawer
2017 Msphere  
Several approaches to the validation of the correctness of the interpretation of crystallographic and NMR data that underlie the models deposited in the PDB are utilized in practice.  ...  Practical, computer-based methods and tools of verification of how well the models adhere to those established structural principles to assure their quality are summarized.  ...  Introduction Biological macromolecules (proteins, as well as other biopolymers, such as nucleic acids and carbohydrates) are composed of atoms belonging to a very limited number of elements (primarily  ... 
doi:10.1007/978-1-4939-7000-1_24 pmid:28573590 pmcid:PMC5560084 fatcat:4umxibvzhvf7ddpc4qfoel33aq

Studying and polishing the PDB's macromolecules

Jane S. Richardson, David C. Richardson
2012 Biopolymers  
The second is that protein and nucleic acid molecules are highly complex and individual, inherently handed and 3-dimensional, and the cooperative and subtle interactions that govern their detailed structure  ...  Ted Hazen, as senior postdoc, did the protein chemistry and heavy-atom derivatives (cloning was decades in the future), developed crystallization conditions, and read the literature.  ...  contributions to these ideas and results, and the PDB and its depositors for those endlessly fascinating structures.  ... 
doi:10.1002/bip.22108 pmid:23023928 pmcid:PMC3535681 fatcat:hpsuf5mlfvek3kww7h74smjzu4

Use of knowledge-based restraints inphenix.refineto improve macromolecular refinement at low resolution

Jeffrey J. Headd, Nathaniel Echols, Pavel V. Afonine, Ralf W. Grosse-Kunstleve, Vincent B. Chen, Nigel W. Moriarty, David C. Richardson, Jane S. Richardson, Paul D. Adams
2012 Acta Crystallographica Section D: Biological Crystallography  
Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted  ...  All three methods show improved MolProbity validation statistics, typically complemented by a lowered R free and a decreased gap between R work and R free .  ...  the cGMP-dependent protein kinase structure set.  ... 
doi:10.1107/s0907444911047834 pmid:22505258 pmcid:PMC3322597 fatcat:uivyd7kpurfe3beheajaq5lrgu

High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH

Ye Tian, Charles D. Schwieters, Stanley J. Opella, Francesca M. Marassi
2016 Journal of Biomolecular NMR  
For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel  ...  Results obtained for NMR-restrained calculations with a set of five soluble proteins and five membrane proteins show that structures calculated with EEFx have significant improvements in accuracy, precision  ...  This research was supported by a grant from the National Institutes of Health (GM118186) and by the Resource for Molecular Imaging of Proteins at UCSD supported by the National Institutes of Health (P41  ... 
doi:10.1007/s10858-016-0082-5 pmid:28035651 pmcid:PMC5487259 fatcat:noxc6xisfzezlc33fsttqjauyq

Improving NMR Structures of RNA

Guillermo A. Bermejo, G. Marius Clore, Charles D. Schwieters
2016 Structure  
Using seven published NMR datasets, RNA-ff1 improves covalent geometry and MolProbity validation criteria for clashes and backbone conformation in most cases, relative to both the previous Xplor-NIH force  ...  geometry, steric contacts, conformation, and RDC-based accuracy SUMMARY Here, we show that modern solution nuclear magnetic resonance (NMR) structures of RNA exhibit more steric clashes and conformational  ...  ACKNOWLEDGMENTS We thank Mijeong Kang and Juli Feigon for kindly providing the Xplor-NIH topology and parameter files associated with the PreQ 1 small-molecule ligand in PDB: 2L1V, and Nico Tjandra's group  ... 
doi:10.1016/j.str.2016.03.007 pmid:27066747 pmcid:PMC4856558 fatcat:sap7p4j4k5gddptdyazi22yupi

New tools provide a second look at HDV ribozyme structure, dynamics and cleavage

Gary J. Kapral, Swati Jain, Jonas Noeske, Jennifer A. Doudna, David C. Richardson, Jane S. Richardson
2014 Nucleic Acids Research  
The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures  ...  However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques  ...  Similar to RNA Rotator, both these tools carry out all-atom contact analysis and other validation in real-time for interactive feedback.  ... 
doi:10.1093/nar/gku992 pmid:25326328 pmcid:PMC4227795 fatcat:qb2jgocvafbx5gvn6jfqhestji

RPF: a quality assessment tool for protein NMR structures

Y. J. Huang, A. Rosato, G. Singh, G. T. Montelione
2012 Nucleic Acids Research  
We describe the RPF web server, a quality assessment tool for protein NMR structures.  ...  the fits of the query structures and random coil structures to these experimental data.  ...  Limitations for analyzing larger size proteins and homodimeric proteins For larger size proteins (e.g. >200 amino acids), it is often necessary to use perdeuterated samples for structure determination.  ... 
doi:10.1093/nar/gks373 pmid:22570414 pmcid:PMC3394279 fatcat:axtrxwk6ebadzcydqbbwhivq2i
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