Pocket Similarity Search using Multiple-Sketches
Names
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Pocket Similarity Search using Multiple-Sketches
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
PoSSuM
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
possum
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
Names
More detailed information about this field from each metasource.
Pocket Similarity Search using Multiple-Sketches
metasource: Fairsharing.orgversion: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
PoSSuM
metasource: Fairsharing.orgversion: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
possum
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.766682
Names
More detailed information about this field from each metasource.
Pocket Similarity Search using Multiple-Sketches
metasource: Fairsharing.orgversion: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
PoSSuM
metasource: Fairsharing.orgversion: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
possum
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.766682
POcket Similarity Search Using Multiple-Sketches (PoSSuM) includes all the discovered protein-small molecule binding site pairs with annotations of various types (e.g., UniProt, CATH, SCOP, SCOPe, EC number and Gene ontology). PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar folds. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures.
Description
More detailed information about this field from each metasource.
POcket Similarity Search Using Multiple-Sketches (PoSSuM) includes all the discovered protein-small molecule binding site pairs with annotations of various types (e.g., UniProt, CATH, SCOP, SCOPe, EC number and Gene ontology). PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar folds. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures.
metasource: Fairsharing.orgversion: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Ligand-binding Pocket Similarity Search using Multiple-Sketches
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
A database of similar protien-ligand binding and putative pockets. Using a novel algorithm, we conducted a large-scale all-pairs search for known and potential binding sites in the Protein Data bank, and discovered over 14 million similar pairs of binding sites.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.766682
Webpage:
http://possum.cbrc.jp/PoSSuM/Webpage
More detailed information about this field from each metasource.
http://possum.cbrc.jp/PoSSuM/
metasource: Fairsharing.orgversion: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
Publications:
Publications
More detailed information about this field from each metasource.
PoSSuM: a database of similar protein-ligand binding and putative pockets
PMID: 22135290
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
PDB-scale analysis of known and putative ligand-binding sites with structural sketches
PMID: 22113700
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs
PMID: 25404129
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gku1144
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.
PoSSuM: a database of similar protein-ligand binding and putative pockets
PMID: 22135290
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
PDB-scale analysis of known and putative ligand-binding sites with structural sketches
PMID: 22113700
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs
PMID: 25404129
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gku1144
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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PoSSuM: a database of similar protein-ligand binding and putative pockets
PubMed citations: 21.
21 articles citing: PoSSuM: a database of similar protein-ligand binding and putative pockets
CavitySpace: A Database of Potential Ligand Binding Sites in the Human Proteome. PMID:35883523
Discovery of novel SARS-CoV-2 inhibitors targeting the main protease Mpro by virtual screenings and hit optimization. PMID:35688349
Computational Methods for Drug Repurposing. PMID:35230686
Novel Computational Approach to Predict Off-Target Interactions for Small Molecules. PMID:33693348
Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot. PMID:31984193
CavBench: A benchmark for protein cavity detection methods. PMID:31609980
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
In silico identification and experimental validation of hits active against KPC-2 β-lactamase. PMID:30496182
A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs). PMID:30408032
Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets. PMID:27924268
Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling. PMID:27807743
Assessing the similarity of ligand binding conformations with the Contact Mode Score. PMID:27620381
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
The Recognition of Identical Ligands by Unrelated Proteins. PMID:26421501
Considerations of Protein Subpockets in Fragment-Based Drug Design. PMID:26307335
A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein. PMID:26222066
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. PMID:25404129
PLIC: protein-ligand interaction clusters. PMID:24763918
Identification of distant drug off-targets by direct superposition of binding pocket surfaces. PMID:24391782
Pocket-based drug design: exploring pocket space. PMID:23180158
ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins. PMID:22600737 -
PDB-scale analysis of known and putative ligand-binding sites with structural sketches
PubMed citations: 11.
11 articles citing: PDB-scale analysis of known and putative ligand-binding sites with structural sketches
End-to-end learning for compound activity prediction based on binding pocket information. PMID:34715777
Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. PMID:29523085
Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins. PMID:28912495
Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets. PMID:27924268
Assessing the similarity of ligand binding conformations with the Contact Mode Score. PMID:27620381
GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution. PMID:27493524
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. PMID:25404129
Pocket-based drug design: exploring pocket space. PMID:23180158
Nanoinformatics: a new area of research in nanomedicine. PMID:22866003
PoSSuM: a database of similar protein-ligand binding and putative pockets. PMID:22135290 -
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs
PubMed citations: 10.
10 articles citing: PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs
Computational Methods for Drug Repurposing. PMID:35230686
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
In silico identification and experimental validation of hits active against KPC-2 β-lactamase. PMID:30496182
Molecular docking analysis of curcumin analogues against kinase domain of ALK5. PMID:29308351
Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics. PMID:29140520
Asymmetric interactions between doublesex and tissue- and sex-specific target genes mediate sexual dimorphism in beetles. PMID:28239147
Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets. PMID:27924268
MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein-ligand fragment interaction, pathways and SNPs. PMID:27131358
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
PatchSurfers: Two methods for local molecular property-based binding ligand prediction. PMID:26427548 - http://dx.doi.org/10.1093/nar/gku1144
Tags:
Tags
More detailed information about this field from each metasource.
ligand binding domain binding
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein binding site prediction
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
small molecule binding
metasource: Fairsharing.org
version: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 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 binding sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
nucleic acid sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
dna binding sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
medicinal chemistry
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.766682
Tags
More detailed information about this field from each metasource.
ligand binding domain binding
metasource: Fairsharing.orgversion: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein binding site prediction
metasource: Fairsharing.orgversion: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
small molecule binding
metasource: Fairsharing.orgversion: FAIRsharing.org: PoSSuM; Pocket Similarity Search using Multiple-Sketches; DOI: https://doi.org/10.25504/FAIRsharing.etqbej; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 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 binding sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.766682
transcription factors and regulatory sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.766682
nucleic acid sites, features and motifs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.766682
dna binding sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.766682
medicinal chemistry
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.766682
ligand binding domain binding protein binding site prediction protein interaction small molecule binding structure protein structure protein binding sites transcription factors and regulatory sites nucleic acid sites, features and motifs dna binding sites medicinal chemistry
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