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Chemical annotation of small and peptide-like molecules at the Protein Data Bank
2013
Database: The Journal of Biological Databases and Curation
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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
2014
Database: The Journal of Biological Databases and Curation
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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
2014
Biopolymers
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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
2020
Scientific Data
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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
2009
Nature Chemical Biology
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(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
2012
Nucleic Acids Research
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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
2009
Nucleic Acids Research
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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
2006
Journal of Integrative Bioinformatics
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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
2012
Journal of Molecular Biology
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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
2011
BMC Genomics
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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
2008
Combinatorial chemistry & high throughput screening
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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
2015
Nucleic Acids Research
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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
2005
Acta Crystallographica Section A Foundations of Crystallography
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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
2012
Nucleic Acids Research
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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
2018
Database: The Journal of Biological Databases and Curation
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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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