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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

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.  ...  of peptide-like antibiotics and inhibitors.  ...  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

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank

Shuchismita Dutta, Dimitris Dimitropoulos, Zukang Feng, Irina Persikova, Sanchayita Sen, Chenghua Shao, John Westbrook, Jasmine Young, Marina A. Zhuravleva, Gerard J. Kleywegt, Helen M. Berman
2014 Biopolymers  
With the accumulation of a large number and variety of molecules in the Protein Data Bank (PDB) comes the need on occasion to review and improve their representation.  ...  For the majority of the single-component molecules, their peptide-like composition was captured in a new representation, called the subcomponent sequence.  ...  peptide-like molecules.  ... 
doi:10.1002/bip.22434 pmid:24173824 pmcid:PMC3992913 fatcat:fsy4z23qcfgnvjj2jpn3stgwta

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

Bioactivity-guided mapping and navigation of chemical space

Steffen Renner, Willem A L van Otterlo, Marta Dominguez Seoane, Sabine Möcklinghoff, Bettina Hofmann, Stefan Wetzel, Ansgar Schuffenhauer, Peter Ertl, Tudor I Oprea, Dieter Steinhilber, Luc Brunsveld, Daniel Rauh (+1 others)
2009 Nature Chemical Biology  
(c,d) Cocrystal structures of proteins and ligands from the scaffold branches of paclitaxel and tubulin (Protein Data Bank code 1JFF) (c) and camptothecin bound to topoisomerase I (Protein Data Bank code  ...  (c,d) Cocrystal structures of proteins and ligands from the scaffold branches of paclitaxel and tubulin (Protein Data Bank code 1JFF) (c) and camptothecin bound to topoisomerase I (Protein Data Bank code  ...  cOMPETIng InTERESTS STATEMEnT The authors declare competing financial interests: details accompany the fulltext HTML version of the paper at http://www.nature.com/naturechemicalbiology/.  ... 
doi:10.1038/nchembio.188 pmid:19561619 fatcat:q2675wgokvh4nmjihxiomb5vga

IUPHAR-DB: updated database content and new features

J. L. Sharman, H. E. Benson, A. J. Pawson, V. Lukito, C. P. Mpamhanga, V. Bombail, A. P. Davenport, J. A. Peters, M. Spedding, A. J. Harmar, NC-IUPHAR
2012 Nucleic Acids Research  
We have described previously the classification and curation of data for small molecule ligands in the database; in this update we have annotated 366 endogenous peptide ligands with their amino acid sequences  ...  We have also matched targets with their endogenous ligands (peptides and small molecules), with particular attention paid to identifying bioactive peptide ligands generated by post-translational modification  ...  ACKNOWLEDGEMENTS The authors thank all contributors and members of NC-IUPHAR and its subcommittees for their ongoing support. NC-IUPHAR members: S.  ... 
doi:10.1093/nar/gks960 pmid:23087376 pmcid:PMC3531077 fatcat:fumahpamvnaftf6fqdfyr67xey

Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites

Benjamin A. Shoemaker, Dachuan Zhang, Ratna R. Thangudu, Manoj Tyagi, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Thomas Madej, Anna R. Panchenko
2009 Nucleic Acids Research  
IBIS provides annotations for different types of binding partners (protein, chemical, nucleic acid and peptides), and facilitates the mapping of a comprehensive biomolecular interaction network for a given  ...  IBIS reports interactions observed in experimentally determined structural complexes of a given protein, and at the same time IBIS infers binding sites/interacting partners by inspecting protein complexes  ...  ACKNOWLEDGEMENTS The authors would like to thank Yanli Wang and Lewis Geer for useful discussions and Eugene Krissinel for help with the PISA software.  ... 
doi:10.1093/nar/gkp842 pmid:19843613 pmcid:PMC2808861 fatcat:ou6b7ft6rfdahfxns6vfbkroge

A structural keystone for drug design

Kristian Rother, Mathias Dunkel, Elke Michalsky, Silke Trissl, Andrean Goede, Ulf Leser, Robert Preissner
2006 Journal of Integrative Bioinformatics  
structures of approved drugs. iii) A conformational library of ligands from the PDB, linking the realms of proteins and small molecules.The data collection contains structures of 30,000 proteins, 5,000  ...  Sets of protein structures can be refined by criteria like protein fold, family, metabolic pathway, resolution and textual annotation.  ...  The second group provides structures of proteins, and here the Protein Data Bank (PDB) [5] is the only player in the field.  ... 
doi:10.1515/jib-2006-19 fatcat:jyng7vcqyje3taz7d5z2t5zxye

Modulating Protein–Protein Interactions with Small Molecules: The Importance of Binding Hotspots

Ratna Rajesh Thangudu, Stephen H. Bryant, Anna R. Panchenko, Thomas Madej
2012 Journal of Molecular Biology  
Honig Keywords: protein structures; molecular interactions; protein-protein interactions; drug development hotspots The modulation of protein-protein interactions (PPIs) by small drug-like molecules is  ...  Here, we propose a scheme that allows performing large-scale screening of all protein complexes and finding putative small-molecule and/or peptide binding sites overlapping with protein-protein binding  ...  Acknowledgements This work was supported by National Institutes of Health/Department of Health and Human Services (Intramural Research Program of the National Library of Medicine).  ... 
doi:10.1016/j.jmb.2011.12.026 pmid:22198293 pmcid:PMC3433052 fatcat:fofx6a7zgreprbztv3epdl6dvy

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

Charles Ansong, Nikola Tolić, Samuel O Purvine, Steffen Porwollik, Marcus Jones, Hyunjin Yoon, Samuel H Payne, Jessica L Martin, Meagan C Burnet, Matthew E Monroe, Pratap Venepally, Richard D Smith (+4 others)
2011 BMC Genomics  
The data provide protein-level experimental validation for approximately half of the predicted protein-coding genes in Salmonella and suggest revisions to several genes that appear to have incorrectly  ...  Our in vivo proteolysis data identified more than 130 signal peptide and N-terminal methionine cleavage events critical for protein function.  ...  This work was supported in part by the National Institute of Allergy and Infectious Diseases NIH/DHHS through interagency agreement Y1-AI-8401-01 (project website http://www.SysBEP.org with links to raw  ... 
doi:10.1186/1471-2164-12-433 pmid:21867535 pmcid:PMC3174948 fatcat:jldhlcg5cjathcm2dnonp3s4yu

A Ligand-Based Approach to Mining the Chemogenomic Space of Drugs

Elisabet Gregori-Puigjane, Jordi Mestres
2008 Combinatorial chemistry & high throughput screening  
The practical implementation and validation of a ligand-based approach to mining the chemogenomic space of drugs is presented and applied to the in silico target profiling of 767 drugs against 684 targets  ...  The detection of cross-pharmacologies between aminergic GPCRs and the opioid, sigma, NMDA, and 5-HT3 receptors aggravate the potential promiscuity of those drugs, predominantly including analgesics, antidepressants  ...  ACKNOWLEDGEMENTS Funding by the Spanish Ministerio de Educación y Ciencia (project reference BIO2005-04171) and the Instituto de Salud Carlos III are kindly acknowledged.  ... 
doi:10.2174/138620708785739952 pmid:18795886 fatcat:cccv64cgt5ciphqyoy6l6wfkny

CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides

Piyush Agrawal, Sherry Bhalla, Salman Sadullah Usmani, Sandeep Singh, Kumardeep Chaudhary, Gajendra P. S. Raghava, Ankur Gautam
2015 Nucleic Acids Research  
The updated data were curated from research papers and patents published in last three years.  ...  In order to understand the structure-function relationship of these peptides, we predicted tertiary structure of CPPs, possessing both modified and natural residues, using state-of-the-art techniques.  ...  ACKNOWLEDGEMENTS Authors are thankful to funding agencies, Council of Scientific and Industrial Research (CSIR) (project Open Source Drug discovery and GENESIS BSC0121), Department of  ... 
doi:10.1093/nar/gkv1266 pmid:26586798 pmcid:PMC4702894 fatcat:h3xgzujao5gpbowa3m55y3tco4

ECRYSTALS(.CHEM.SOTON.AC.UK): open archive publication of crystal structure data

M. B. Hursthouse, S. J. Coles, J. G. Frey, L. Carr, C. Gutteridge, L. Lyon, R. Heery, M. Duke, M. Day
2005 Acta Crystallographica Section A Foundations of Crystallography  
The reader will hopefully gain an insight into a service utilizing the most successful small molecule synchrotron beam line in the world.  ...  the use of station 9.8 at Daresbury laboratory.  ...  The Protein Data Bank has traditionally offered only text-based query services. These tools are very powerful in the hands of experts when the data entries have been well annotated.  ... 
doi:10.1107/s0108767305080013 fatcat:c3knhyodcjd5li4gtyyv2ydh2a

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

Jianyi Yang, Ambrish Roy, Yang Zhang
2012 Nucleic Acids Research  
Most ligand-binding sites prediction methods use the protein structures from the Protein Data Bank (PDB) as templates.  ...  However, not all ligands present in the PDB are biologically relevant, as small molecules are often used as additives for solving the protein structures.  ...  Three types of ligand molecules are collected in the BioLiP database: the molecules from the 'HETATM' record (excluding water and modified residues), small DNA/RNA and peptides with <30 residues.  ... 
doi:10.1093/nar/gks966 pmid:23087378 pmcid:PMC3531193 fatcat:oxdg7gtdljdc3i7whmo4bwlzge

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi (+39 others)
2018 Database: The Journal of Biological Databases and Curation  
Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands.  ...  Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.  ...  Acknowledgements The authors thank all the members of the worldwide Protein Data Bank (wwPDB) for their support and feedback, Kim Henrick for his direction to the PDB in Europe (PDBe) biocuration team  ... 
doi:10.1093/database/bay002 pmid:29688351 pmcid:PMC5804564 fatcat:pymncvy65zghjgdhleavnz7oce
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