Recognition of functional sites in protein structures. (Q30341546)

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English	Recognition of functional sites in protein structures.	scientific article

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Europe PubMed Central

PubMed publication ID

15147845

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20 June 2017

title

Recognition of functional sites in protein structures. (English)

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PubMed publication ID

15147845

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20 June 2017

author

Ruth Nussinov

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2

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Ruth Nussinov

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Europe PubMed Central

PubMed publication ID

15147845

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20 June 2017

Haim Wolfson

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3

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Haim J Wolfson

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Europe PubMed Central

PubMed publication ID

15147845

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20 June 2017

author name string

Alexandra Shulman-Peleg

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1

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Europe PubMed Central

PubMed publication ID

15147845

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20 June 2017

language of work or name

English

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publication date

1 June 2004

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Europe PubMed Central

PubMed publication ID

15147845

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20 June 2017

published in

Journal of Molecular Biology

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Europe PubMed Central

PubMed publication ID

15147845

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20 June 2017

volume

339

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Europe PubMed Central

PubMed publication ID

15147845

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20 June 2017

issue

3

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Europe PubMed Central

PubMed publication ID

15147845

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20 June 2017

page(s)

607-633

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Europe PubMed Central

PubMed publication ID

15147845

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20 June 2017

cites work

The ASTRAL compendium for protein structure and sequence analysis

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PubMed

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Structure comparison and structure patterns

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking

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Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

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One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions

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PubMed

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Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases

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ASTRAL compendium enhancements

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

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Searching for functional sites in protein structures.

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

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Protein recognition of adenylate: an example of a fuzzy recognition template

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12 December 2020

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Detection and geometric modeling of molecular surfaces and cavities using digital mathematical morphological operations

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PubMed

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Crystal structures of adenine phosphoribosyltransferase from Leishmania donovani

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Lipid-binding proteins: a family of fatty acid and retinoid transport proteins

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A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures

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12 December 2020

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High‐resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer

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Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins.

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Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations

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The Protein Data Bank

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Fast prediction and visualization of protein binding pockets with PASS.

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An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.

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Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes

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CASTp: Computed Atlas of Surface Topography of proteins

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Principles of docking: An overview of search algorithms and a guide to scoring functions

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PubMed

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The ASTRAL Compendium in 2004

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

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

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The structure of Staphylococcus aureus epidermolytic toxin A, an atypic serine protease, at 1.7 A resolution

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

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Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

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A consensus-binding structure for adenine at the atomic level permits searching for the ligand site in a wide spectrum of adenine-containing complexes

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

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

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

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Virtual screening: an effective tool for lead structure discovery?

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

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Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design

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PubMed

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The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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Crystal structure and thermodynamic analysis of human brain fatty acid-binding protein

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

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Inferring functional relationships of proteins from local sequence and spatial surface patterns

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

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Structure-based identification of a novel NTPase from Methanococcus jannaschii

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The crystal structure of the liver fatty acid-binding protein. A complex with two bound oleates

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PubMed

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Molecular shape comparisons in searches for active sites and functional similarity

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identification of protein functions from a molecular surface database, eF-site.

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular recognition via face center representation of a molecular surface

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics

1 reference

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

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High-throughput docking for lead generation

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A method for simultaneous alignment of multiple protein structures

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A computer vision based technique for 3-D sequence-independent structural comparison of proteins

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Computational methods for the structural alignment of molecules

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

BioInfo3D: a suite of tools for structural bioinformatics

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A geometric approach to macromolecule-ligand interactions

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Searching for patterns of amino acids in 3D protein structures

1 reference

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

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A review of protein-small molecule docking methods

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https://pubmed.ncbi.nlm.nih.gov/15147845

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based on heuristic

inferred from PubMed ID database lookup

Identification of protein biochemical functions by similarity search using the molecular surface database eF-site

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

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

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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based on heuristic

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Molecular surface representations by sparse critical points

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Solvent-accessible surfaces of proteins and nucleic acids

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PubMed

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based on heuristic

inferred from PubMed ID database lookup

Sequence and structural analysis of cellular retinoic acid-binding proteins reveals a network of conserved hydrophobic interactions

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/15147845

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/15147845

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

DOI

10.1016/J.JMB.2004.04.012

1 reference

stated in

Europe PubMed Central

PubMed publication ID

15147845

retrieved

20 June 2017

PubMed publication ID

15147845

1 reference

stated in

Europe PubMed Central

PubMed publication ID

15147845

retrieved

20 June 2017

ResearchGate publication ID

8558023

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