Protein pockets: inventory, shape, and comparison (Q30494235)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20205445%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

title

Protein pockets: inventory, shape, and comparison (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20205445%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20205445%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

Kim A Sharp

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20205445%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

publication date

1 April 2010

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20205445%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Information and Modeling

19 January 2020

published in

1 reference

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19 January 2020

volume

1 reference

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19 January 2020

issue

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20205445%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

page(s)

589-603

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20205445%20AND%20SRC:MED&resulttype=core&format=json

Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.

19 January 2020

cites work

1 reference

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Shape and evolution of thermostable protein structure.

20 June 2018

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Identifying and characterizing binding sites and assessing druggability

20 June 2018

1 reference

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Docking for fragment inhibitors of AmpC -lactamase

20 June 2018

1 reference

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Accurate prediction of peptide binding sites on protein surfaces.

20 June 2018

1 reference

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Molecular docking and ligand specificity in fragment-based inhibitor discovery

20 June 2018

1 reference

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Comprehensive structural classification of ligand-binding motifs in proteins

20 June 2018

1 reference

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Protein promiscuity and its implications for biotechnology

20 June 2018

1 reference

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The importance of discerning shape in molecular pharmacology

20 June 2018

1 reference

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Predicting druggable binding sites at the protein-protein interface.

20 June 2018

1 reference

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Prediction of specificity-determining residues for small-molecule kinase inhibitors

20 June 2018

1 reference

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Can morphing methods predict intermediate structures?

20 June 2018

1 reference

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Finding and characterizing tunnels in macromolecules with application to ion channels and pores.

20 June 2018

1 reference

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Small molecular weight protein-protein interaction antagonists: an insurmountable challenge?

20 June 2018

1 reference

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Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.

20 June 2018

1 reference

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Quantifying the relationships among drug classes

20 June 2018

1 reference

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Fast dynamics perturbation analysis for prediction of protein functional sites

20 June 2018

1 reference

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Reaching for high-hanging fruit in drug discovery at protein-protein interfaces

20 June 2018

1 reference

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In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Intrinsic motions along an enzymatic reaction trajectory

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

The SeeDs approach: integrating fragments into drug discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

PocketDepth: a new depth based algorithm for identification of ligand binding sites in proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

PocketPicker: analysis of ligand binding-sites with shape descriptors.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Structure-based activity prediction for an enzyme of unknown function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Informatics and modeling challenges in fragment-based drug discovery.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

HotPatch: a statistical approach to finding biologically relevant features on protein surfaces

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Shape variation in protein binding pockets and their ligands

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Relating protein pharmacology by ligand chemistry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Computational identification of inhibitors of protein-protein interactions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

On the nature of cavities on protein surfaces: application to the identification of drug-binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

SitesBase: a database for structure-based protein-ligand binding site comparisons

20 June 2018

1 reference

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Charting biologically relevant chemical space: a structural classification of natural products (SCONP)

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction

20 June 2018

1 reference

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ZINC--a free database of commercially available compounds for virtual screening

20 June 2018

1 reference

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Searching for new allosteric sites in enzymes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

A computational method for the analysis and prediction of protein:phosphopeptide-binding sites.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Structure-guided fragment screening for lead discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Discovery of an allosteric site in the caspases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Detection, delineation, measurement and display of cavities in macromolecular structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Fragment screening and assembly: a highly efficient approach to a selective and cell active protein tyrosine phosphatase 1B inhibitor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Ligand binding: functional site location, similarity and docking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Discovery and Structure−Activity Relationship of Oxalylarylaminobenzoic Acids as Inhibitors of Protein Tyrosine Phosphatase 1B

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Evolutionary predictions of binding surfaces and interactions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

20 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B: A paradigm for inhibitor design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Protein clefts in molecular recognition and function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Refined 1.7 A X-ray crystallographic structure of P-30 protein, an amphibian ribonuclease with anti-tumor activity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Water: now you see it, now you don't

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

A geometric approach to macromolecule-ligand interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Solvent-accessible surfaces of proteins and nucleic acids

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: Indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 Å resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

In search of new lead compounds for trypanosomiasis drug design: a protein structure-based linked-fragment approach.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Identification of small-molecule inhibitors of the JIP-JNK interaction

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Merging chemical and biological space: Structural mapping of enzyme binding pocket space.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Building alternate protein structures using the elastic network model.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Molecular docking for substrate identification: the short-chain dehydrogenases/reductases

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Automated prediction of ligand-binding sites in proteins

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Transient Pockets on Protein Surfaces Involved in Protein−Protein Interaction

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Structure-based maximal affinity model predicts small-molecule druggability.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Travel depth, a new shape descriptor for macromolecules: application to ligand binding.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Comparison of protein active site structures for functional annotation of proteins and drug design

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Conformational diversity of ligands bound to proteins

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

A method for localizing ligand binding pockets in protein structures

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

An intuitive approach to measuring protein surface curvature.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

A new method to detect related function among proteins independent of sequence and fold homology.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Fast prediction and visualization of protein binding pockets with PASS.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Molecular shape comparisons in searches for active sites and functional similarity

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859996

Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20205445

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structure-based identification of small molecule binding sites using a free energy model

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20205445

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CI900397T

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20205445%20AND%20SRC:MED&resulttype=core&format=json

journals/jcisd/ColemanS10

19 January 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20205445%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

PubMed publication ID

20205445

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20205445%20AND%20SRC:MED&resulttype=core&format=json