(Q30362321)

10 August 2017

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

1 reference

10 August 2017

1 reference

2

Philip E Bourne

0 references

Lei Xie

series ordinal

1

object named as

Lei Xie

1 reference

PMCID

1892088

10 August 2017

language of work or name

1 reference

22 May 2007

1 reference

10 August 2017

1 reference

10 August 2017

8 Suppl 4

1 reference

10 August 2017

S9

1 reference

Creative Commons Attribution 2.0 Generic

10 August 2017

start time

1 May 2007

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1186/1471-2105-8-s4-s9

0 references

cites work

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Classification of chemical compounds by protein-compound docking for use in designing a focused library.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Accounting for global protein deformability during protein-protein and protein-ligand docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Predicting protein function from sequence and structural data.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Pocketome via comprehensive identification and classification of ligand binding envelopes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Comprehensive identification of "druggable" protein ligand binding sites.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Conformational changes observed in enzyme crystal structures upon substrate binding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Predicting protein functional sites with phylogenetic motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Ligand binding: functional site location, similarity and docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

SuperStar: improved knowledge-based interaction fields for protein binding sites

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Analysis of protein-protein interaction sites using surface patches

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Automatic identification and representation of protein binding sites for molecular docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

An evolutionary trace method defines binding surfaces common to protein families

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Classical electrostatics in biology and chemistry

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

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=1892088

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=1892088

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=1892088

Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

In silico identification of functional regions 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=1892088

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Network Analysis of Protein Structures Identifies Functional Residues

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Identification of substrate binding sites in enzymes by computational solvent mapping.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

Identification of ligand binding sites on proteins using a multi-scale approach.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

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=1892088

Small molecule recognition: solid angles surface representation and molecular shape complementarity.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

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=1892088

Surface solid angle-based site points for molecular docking

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1892088

A new method for estimating the importance of hydrophobic groups in the binding site of a protein

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17570152

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Coarse and reliable geometric alignment for protein docking

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17570152

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A virtual active compound produced from the negative image of a ligand-binding pocket, and its application to in-silico drug screening

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17570152

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-8-S4-S9

1 reference

10 August 2017

journals/bmcbi/XieB07

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

10 August 2017

1 reference

PMCID

1892088