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Small molecule annotation for the Protein Data Bank

S. Sen, J. Young, J. M. Berrisford, M. Chen, M. J. Conroy, S. Dutta, L. Di Costanzo, G. Gao, S. Ghosh, B. P. Hudson, R. Igarashi, Y. Kengaku (+11 others)
2014 Database: The Journal of Biological Databases and Curation  
Small molecule annotation for the protein data bank.  ...  Abstract The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100 000 structures contain more  ...  Acknowledgements The 3D images in the manuscript were generated using PyMOL (29) . The authors are grateful to Prof. Gerard Kleywegt for helpful comments on this manuscript. Conflict of interest.  ... 
doi:10.1093/database/bau116 pmid:25425036 pmcid:PMC4243272 fatcat:k2ru4exflrd4bhldwpvxh4anwy

Enhancing small-molecule information in the Protein Data Bank in Europe

Lukáš Pravda, The PDBe
2019 Acta Crystallographica Section A: Foundations and Advances  
The Protein Data Bank (PDB) provides a wealth of data on biomacromolecules and their complexes with small molecules/ligands.  ...  Interaction information between macromolecules and small molecules is already available through the new aggregated views for proteins [2] which are part of the Protein Data Bank in Europe Knowledge Base  ...  The Protein Data Bank (PDB) provides a wealth of data on biomacromolecules and their complexes with small molecules/ligands.  ... 
doi:10.1107/s2053273319093707 fatcat:juao2qiysndzffkqkeop3lpwmu

Annotation and Curation of the Protein Data Bank

Jasmine Young, RCSB PDBj PDBe Protein Data Bank
2009 Nature Precedings  
way Abstract The Protein Data Bank (PDB) is the worldwide repository for experimentally determined 3D structures of biological macromolecules.  ...  To maintain the highest standards in curation and processing, the members of the worldwide Protein Data Bank (wwPDB) collaborate in data annotation and the development of procedures, tools, and resources  ... 
doi:10.1038/npre.2009.3379.1 fatcat:w5tg7kmykvcknalmldp7gippny

Integration of chemical information with protein sequences and 3D structures

Adel Golovin, K Henrick, G Kleywegt
2010 Journal of Cheminformatics  
The Protein Data Bank (PDB) contains a wealth of small molecule -macro molecule complexes the study of which contribute enormously to our understanding of the interactions.  ...  One such method is PDBeMotif, that has been developed by the Protein Data Bank in Europe (PDBe) at EMBL-EBI.  ...  The Protein Data Bank (PDB) contains a wealth of small molecule -macro molecule complexes the study of which contribute enormously to our understanding of the interactions.  ... 
doi:10.1186/1758-2946-2-s1-o17 pmcid:PMC2867125 fatcat:vzp5dl7xobcszbn6hheum4zzju

Finding enzyme cofactors in Protein Data Bank

Abhik Mukhopadhyay, Neera Borkakoti, Lukas Pravda, Jonathan D Tyzack, Janet M Thornton, Sameer Velankar, Jonathan Wren
2019 Bioinformatics  
Cofactors are essential for many enzyme reactions. The Protein Data Bank (PDB) contains >67 000 entries containing enzyme structures, many with bound cofactor or cofactor-like molecules.  ...  The Protein Data Bank in Europe (PDBe; pdbe.org) has implemented a pipeline to identify enzyme cofactor and cofactor-like molecules, which are now part of the PDBe weekly release process.  ...  Acknowledgements We thank Gemma Holliday and Antonio Ribeiro for their scientific and technical support.  ... 
doi:10.1093/bioinformatics/btz115 pmid:30759194 pmcid:PMC6748742 fatcat:egqdkksxljcybig4s4tdfoukai

PDBe-KB: a community-driven resource for structural and functional annotations

2019 Nucleic Acids Research  
and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB).  ...  The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural  ...  We would like to thank the UniProt and Inter-Pro teams for their contributions on the ProtVista sequence feature viewer as well as with certain annotations.  ... 
doi:10.1093/nar/gkz853 pmid:31584092 pmcid:PMC6943075 fatcat:lbpb4ss3ynaetnusqksvrbjy6y

The European Bioinformatics Institute's data resources: towards systems biology

C. Brooksbank
2004 Nucleic Acids Research  
Acids Research, we have launched new databases covering protein-protein interactions (IntAct), pathways (Reactome) and small molecules (ChEBI).  ...  different data types, thereby helping them to put the parts together to understand biology at the systems level.  ...  The EBI's most recently launched database bridges the gap between the world of proteins and that of small molecules.  ... 
doi:10.1093/nar/gki026 pmid:15608238 pmcid:PMC539980 fatcat:ccwgkwuws5fsjaz7zp7i5jfjzy

Chemical annotation of small and peptide-like molecules at the Protein Data Bank

Jasmine Y. Young, Zukang Feng, Dimitris Dimitropoulos, Raul Sala, John Westbrook, Marina Zhuravleva, Chenghua Shao, Martha Quesada, Ezra Peisach, Helen M. Berman
2013 Database: The Journal of Biological Databases and Curation  
They also thank their collaborators in the wwPDB (Protein Data Bank in Europe, Protein Data Bank Japan and BioMagResBank) for their input and testing of this module. Conflict of interest.  ...  Acknowledgements The authors are grateful to Rachel Kramer Green and Christine Zardecki for their helpful comments on this manuscript.  ...  (2) , Protein Data Bank in Europe (3) and Protein Data Bank Japan (4) ].  ... 
doi:10.1093/database/bat079 pmid:24291661 pmcid:PMC3843158 fatcat:fcw46qnbfbhe5cjpxb7x7etiea

MMDB: 3D structures and macromolecular interactions

T. Madej, K. J. Addess, J. H. Fong, L. Y. Geer, R. C. Geer, C. J. Lanczycki, C. Liu, S. Lu, A. Marchler-Bauer, A. R. Panchenko, J. Chen, P. A. Thiessen (+3 others)
2011 Nucleic Acids Research  
MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank.  ...  It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access  ...  unit as the set of data submitted to the Protein Data Bank by the depositor.  ... 
doi:10.1093/nar/gkr1162 pmid:22135289 pmcid:PMC3245041 fatcat:63sbhrttvngx7axcs36yxdccly

Knowledge-based annotation of small molecule binding sites in proteins

Ratna R Thangudu, Manoj Tyagi, Benjamin A Shoemaker, Stephen H Bryant, Anna R Panchenko, Thomas Madej
2010 BMC Bioinformatics  
The study of protein-small molecule interactions is vital for understanding protein function and for practical applications in drug discovery.  ...  Results: We have developed a new method for the annotation of protein-small molecule binding sites, using inference by homology, which allows us to extend annotation onto protein sequences without experimental  ...  Author Details National Center for Biotechnology Information, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894 USA  ... 
doi:10.1186/1471-2105-11-365 pmid:20594344 pmcid:PMC2909224 fatcat:em4aumldr5acvds6d2f3qpzone

The Protein Data Bank archive as an open data resource

Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley
2014 Journal of Computer-Aided Molecular Design  
The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012).  ...  An analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources  ...  Acknowledgments The wwPDB thanks all staff members past and present, and all members of the PDB community.  ... 
doi:10.1007/s10822-014-9770-y pmid:25062767 pmcid:PMC4196035 fatcat:yhd3biuk5relpdwfijmmiliyk4

The Protein Data Bank in Europe (PDBe): bringing structure to biology

Sameer Velankar, Gerard J. Kleywegt
2011 Acta Crystallographica Section D: Biological Crystallography  
The deposition sites curate (i.e. annotate, enrich and validate) the structures and the data and make them available in the Protein Data Bank (PDB; Bernstein et al., 1977; Berman, 2008) .  ...  et al., 2005; Tagari et al., 2006) , is the European partner in the Worldwide Protein Data Bank (wwPDB; http:// wwpdb.org; Berman et al., 2007) .  ... 
doi:10.1107/s090744491004117x pmid:21460450 pmcid:PMC3069747 fatcat:gpse5hxwwvbyxbqhrrsodahkye

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Saqib Mir, Younes Alhroub, Stephen Anyango, David R Armstrong, John M Berrisford, Alice R Clark, Matthew J Conroy, Jose M Dana, Mandar Deshpande, Deepti Gupta, Aleksandras Gutmanas, Pauline Haslam (+10 others)
2017 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data.  ...  The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and  ...  ACKNOWLEDGEMENTS We would like to thank all collaborators and partners at the EMBL-EBI, EMBL, wwPDB, EMDB, CCP4, SASBDB, CCPN, CCDC, CEITEC, MRC-LMB and other collaborative efforts, as well as the structural  ... 
doi:10.1093/nar/gkx1070 pmid:29126160 pmcid:PMC5753225 fatcat:j6ocp5cauvau3d7jd4gw3htwiq

Probabilistic identification of saccharide moieties in biomolecules and their protein complexes

Hesam Dashti, William M. Westler, Jonathan R. Wedell, Olga V. Demler, Hamid R. Eghbalnia, John L. Markley, Samia Mora
2020 Scientific Data  
CTPIC analysis of the RCSB Ligand Expo (database of small molecules found to bind proteins in the Protein Data Bank) led to a substantial increase in the number of ligands characterized as saccharides.  ...  CTPIC analysis of Protein Data Bank identified 7.7% of the proteins as saccharide-binding. CTPIC is freely available as a webservice at (http://ctpic.nmrfam.wisc.edu).  ...  Protein Data Bank (PDB) [19] [20] [21] , RCSB PDB Ligand Expo 22 , CCMRD 23 , and the KEGG glycan database 24 .  ... 
doi:10.1038/s41597-020-0547-y pmid:32620933 pmcid:PMC7335193 fatcat:vftwcv2agfhwlc6bqxymctbylq

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

Sameer Velankar, Glen van Ginkel, Younes Alhroub, Gary M. Battle, John M. Berrisford, Matthew J. Conroy, Jose M. Dana, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Pieter M. S. Hendrickx, Ingvar Lagerstedt (+21 others)
2015 Nucleic Acids Research  
The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information  ...  A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality  ...  ACKNOWLEDGEMENTS We would like to thank all collaborators and partners at the EMBL-EBI, EMBL, wwPDB, EMDataBank, CCP4, CCPN, CCDC and other collaborative efforts, as well as the structural biology and  ... 
doi:10.1093/nar/gkv1047 pmid:26476444 pmcid:PMC4702783 fatcat:sqjtb2p3drbjncdycqrfr3m2lm
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