(Q30402719)

7 November 2017

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins (English)

1 reference

7 November 2017

1 reference

Kuan Pern Tan

1

1 reference

7 November 2017

Raghavan Varadarajan

series ordinal

2

1 reference

7 November 2017

M S Madhusudhan

series ordinal

3

1 reference

7 November 2017

language of work or name

English

0 references

publication date

16 May 2011

1 reference

7 November 2017

Nucleic Acids Research

1 reference

7 November 2017

39

1 reference

7 November 2017

Web Server issue

1 reference

7 November 2017

W242-8

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

7 November 2017

start time

14 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

In silico prediction of binding sites on proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

Fpocket: an open source platform for ligand pocket detection.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

LigASite--a database of biologically relevant binding sites in proteins with known apo-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=3125764

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=3125764

Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

The "first in-last out" hypothesis on protein folding revisited

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

Pocketome via comprehensive identification and classification of ligand binding envelopes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

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=3125764

Atom depth in protein structure 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=3125764

Atom depth as a descriptor of the protein interior

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

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=3125764

Residue depth: a novel parameter for the analysis of protein structure and stability.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

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=3125764

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

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=3125764

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=3125764

The interpretation of protein structures: Estimation of static accessibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

Cavity search: an algorithm for the isolation and display of cavity-like binding regions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino 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=3125764

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

Large-scale comparison of four binding site detection algorithms.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

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=3125764

LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active 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=3125764

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=3125764

PQS: a protein quaternary structure file server

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

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=3125764

A new approach to the automatic identification of candidates for ligand receptor sites in proteins: (I). Search for pocket regions.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125764

Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21576233

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Finding and filling protein cavities using cellular logic operations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21576233

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A nuclear magnetic resonance study of the hydrogen-exchange behaviour of lysozyme in crystals and solution

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21576233

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKR356

1 reference

7 November 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

7 November 2017

PubMed publication ID

21576233

1 reference