Pocketome: an encyclopedia of small-molecule binding sites in 4D
Names
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Pocketome: an encyclopedia of small-molecule binding sites in 4D
metasource: Fairsharing.org
version: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Pocketome
metasource: Fairsharing.org
version: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293
pocketome
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293
Names
More detailed information about this field from each metasource.
Pocketome: an encyclopedia of small-molecule binding sites in 4D
metasource: Fairsharing.orgversion: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Pocketome
metasource: Fairsharing.orgversion: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293
pocketome
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:10.100293
Other names: Pocketome, pocketome
Names
More detailed information about this field from each metasource.
Pocketome: an encyclopedia of small-molecule binding sites in 4D
metasource: Fairsharing.orgversion: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Pocketome
metasource: Fairsharing.orgversion: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293
pocketome
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:10.100293
This source may no longer be available. No known URL could be resolved successfully.
The Pocketome is an encyclopedia of conformational ensembles of druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry describes a site on a protein surface that is involved in transient interactions with small molecules and peptides.
Description
More detailed information about this field from each metasource.
The Pocketome is an encyclopedia of conformational ensembles of druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry describes a site on a protein surface that is involved in transient interactions with small molecules and peptides.
metasource: Fairsharing.orgversion: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Small-molecule and/or peptide binding pockets in the structural proteome
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
To assist in understanding the flexible protein-ligand interactions, we constructed this tool, an encyclopedia of about one thousand experimentally solved conformational ensembles of druggable binding sites in proteins, grouped by location and consistent chain/cofactor composition. The core of it is derived regularly from the Protein Data Bank and the Uniprot Knowledgebase.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:10.100293
Webpage:
http://pocketome.orgWebpage
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http://pocketome.org
metasource: Fairsharing.orgversion: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://www.pocketome.org
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://www.pocketome.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:10.100293
Publications:
Publications
More detailed information about this field from each metasource.
Pocketome: an encyclopedia of small-molecule binding sites in 4D
PMID: 22080553
metasource: Fairsharing.org
version: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293
The flexible pocketome engine for structural chemogenomics
PMID: 19727619
metasource: Fairsharing.org
version: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/GKR825
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Pocketome: an encyclopedia of small-molecule binding sites in 4D
PMID: 22080553
metasource: Fairsharing.org
version: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293
The flexible pocketome engine for structural chemogenomics
PMID: 19727619
metasource: Fairsharing.org
version: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/GKR825
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Pocketome: an encyclopedia of small-molecule binding sites in 4D
PubMed citations: 63.
63 articles citing: Pocketome: an encyclopedia of small-molecule binding sites in 4D
CavitySpace: A Database of Potential Ligand Binding Sites in the Human Proteome. PMID:35883523
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision. PMID:34814950
2D SIFt: a matrix of ligand-receptor interactions. PMID:34496955
Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism. PMID:34192090
Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises. PMID:33936562
A new microtubule-stabilizing agent shows potent antiviral effects against African swine fever virus with no cytotoxicity. PMID:33706677
Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design. PMID:32865404
Synthesis, Optimization, Antifungal Activity, Selectivity, and CYP51 Binding of New 2-Aryl-3-azolyl-1-indolyl-propan-2-ols. PMID:32784450
Unraveling Plant Natural Chemical Diversity for Drug Discovery Purposes. PMID:32317969
visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level. PMID:32164574
HIV-1 fusion inhibitors targeting the membrane-proximal external region of Env spikes. PMID:32152540
Druggable exosites of the human kino-pocketome. PMID:31925639
CavBench: A benchmark for protein cavity detection methods. PMID:31609980
Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4. PMID:31598897
Molecular Docking: Shifting Paradigms in Drug Discovery. PMID:31487867
High Impact: The Role of Promiscuous Binding Sites in Polypharmacology. PMID:31295958
Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing. PMID:31125569
Extended Multitarget Pharmacology of Anticancer Drugs. PMID:31025863
2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site. PMID:30689953
Protein pocket detection via convex hull surface evolution and associated Reeb graph. PMID:30423105
A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs). PMID:30408032
GPCR homology model template selection benchmarking: Global versus local similarity measures. PMID:30390544
Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3. PMID:30094533
SynPharm: A Guide to PHARMACOLOGY Database Tool for Designing Drug Control into Engineered Proteins. PMID:30087931
Convolutional neural network scoring and minimization in the D3R 2017 community challenge. PMID:29992528
Toward Small-Molecule Inhibition of Protein-Protein Interactions: General Aspects and Recent Progress in Targeting Costimulatory and Coinhibitory (Immune Checkpoint) Interactions. PMID:29848279
Exploring G Protein-Coupled Receptors (GPCRs) Ligand Space via Cheminformatics Approaches: Impact on Rational Drug Design. PMID:29593527
Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates. PMID:29551288
Convergence of Wnt, growth factor, and heterotrimeric G protein signals on the guanine nucleotide exchange factor Daple. PMID:29487190
The anthelmintic praziquantel is a human serotoninergic G-protein-coupled receptor ligand. PMID:29208933
Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens. PMID:28948099
Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins. PMID:28912495
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach. PMID:28887659
Protein structural motifs in prediction and design. PMID:28460216
Normal Modes Expose Active Sites in Enzymes. PMID:28002427
Orphan receptor ligand discovery by pickpocketing pharmacological neighbors. PMID:27992882
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. PMID:27074285
Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. PMID:26807783
Historeceptomic Fingerprints for Drug-Like Compounds. PMID:26733872
Structure-based predictions of activity cliffs. PMID:25918827
Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics. PMID:25414519
Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping. PMID:25407367
Assessing variation in the potential susceptibility of fish to pharmaceuticals, considering evolutionary differences in their physiology and ecology. PMID:25405965
Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. PMID:25378330
sc-PDB: a 3D-database of ligandable binding sites--10 years on. PMID:25300483
Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. PMID:25254076
Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility. PMID:25079060
In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α. PMID:24928891
Towards structural systems pharmacology to study complex diseases and personalized medicine. PMID:24830652
PLIC: protein-ligand interaction clusters. PMID:24763918
PeptiSite: a structural database of peptide binding sites in 4D. PMID:24406170
In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. PMID:24392850
ASD v2.0: updated content and novel features focusing on allosteric regulation. PMID:24293647
A comprehensive survey of small-molecule binding pockets in proteins. PMID:24204237
Molecular basis for benzodiazepine agonist action at the type 1 cholecystokinin receptor. PMID:23754289
Pivotal role of P450-P450 interactions in CYP3A4 allostery: the case of α-naphthoflavone. PMID:23651100
LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites. PMID:23609546
Pocket-based drug design: exploring pocket space. PMID:23180158
Compound activity prediction using models of binding pockets or ligand properties in 3D. PMID:23116466
Can the energy gap in the protein-ligand binding energy landscape be used as a descriptor in virtual ligand screening? PMID:23071584
Small molecule inhibitors of Bacillus anthracis protective antigen proteolytic activation and oligomerization. PMID:22954387
ALiBERO: evolving a team of complementary pocket conformations rather than a single leader. PMID:22947092
Docking and scoring with ICM: the benchmarking results and strategies for improvement. PMID:22569591 -
The flexible pocketome engine for structural chemogenomics
PubMed citations: 25.
25 articles citing: The flexible pocketome engine for structural chemogenomics
Inhibition of bacterial and human zinc-metalloproteases by bisphosphonate- and catechol-containing compounds. PMID:33757387
Functional and druggability analysis of the SARS-CoV-2 proteome. PMID:33137330
Druggable exosites of the human kino-pocketome. PMID:31925639
Evidence for ligandable sites in structured RNA throughout the Protein Data Bank. PMID:30982658
In silico discovery of small molecules that inhibit RfaH recruitment to RNA polymerase. PMID:30069925
Privileged Structures Revisited. PMID:28558125
Allosteric modulation model of the mu opioid receptor by herkinorin, a potent not alkaloidal agonist. PMID:28364251
How special is the biochemical function of native proteins? PMID:26962440
Identifying ligands at orphan GPCRs: current status using structure-based approaches. PMID:26837045
Historeceptomic Fingerprints for Drug-Like Compounds. PMID:26733872
Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping. PMID:25407367
HDAC8 and STAT3 repress BMF gene activity in colon cancer cells. PMID:25321483
PeptiSite: a structural database of peptide binding sites in 4D. PMID:24406170
Can the energy gap in the protein-ligand binding energy landscape be used as a descriptor in virtual ligand screening? PMID:23071584
Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies. PMID:22380603
Methods of protein structure comparison. PMID:22323224
Pocketome: an encyclopedia of small-molecule binding sites in 4D. PMID:22080553
Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol. PMID:22071255
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. PMID:21827947
Systematic exploitation of multiple receptor conformations for virtual ligand screening. PMID:21625529
Molecular recognition in the case of flexible targets. PMID:21619526
Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library. PMID:21064162
A protein sequence meta-functional signature for calcium binding residue prediction. PMID:20824111
Ligand binding and subtype selectivity of the human A(2A) adenosine receptor: identification and characterization of essential amino acid residues. PMID:20147292
Recipes for the selection of experimental protein conformations for virtual screening. PMID:20000587 - http://dx.doi.org/10.1093/nar/GKR825
Tags:
Tags
More detailed information about this field from each metasource.
binding site
metasource: Fairsharing.org
version: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein structure
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293
protein binding sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293
nucleic acid sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293
dna binding sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293
Tags
More detailed information about this field from each metasource.
binding site
metasource: Fairsharing.orgversion: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: Pocketome; Pocketome: an encyclopedia of small-molecule binding sites in 4D; DOI: https://doi.org/10.25504/FAIRsharing.tc6df8; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
structure databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein structure
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein interactions
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:10.100293
protein binding sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:10.100293
nucleic acid sites, features and motifs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:10.100293
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:10.100293
dna binding sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:10.100293
binding site protein interaction small molecule structure polypeptide region structure protein structure protein interaction protein binding sites nucleic acid sites, features and motifs molecular interactions, pathways and networks dna binding sites
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