(Q34247981)

31 July 2017

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities (English)

1 reference

31 July 2017

1 reference

Manuela Helmer-Citterich

series ordinal

3

object named as

Manuela Helmer-Citterich

1 reference

31 July 2017

4

Gabriele Ausiello

1 reference

PubMed ID

22536963

31 July 2017

Pier Federico Gherardini

series ordinal

2

object named as

Pier Federico Gherardini

1 reference

31 July 2017

1

Valerio Bianchi

1 reference

31 July 2017

28 March 2012

1 reference

31 July 2017

1 reference

31 July 2017

13 Suppl 4

1 reference

31 July 2017

S17

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2105-13-s4-s17

31 July 2017

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

Superpose3D: a local structural comparison program that allows for user-defined structure representations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

3DLigandSite: predicting ligand-binding sites using similar structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

Ligand-binding site prediction of proteins based on known fragment-fragment interactions.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

Modular architecture of nucleotide-binding pockets.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

Structural motifs recurring in different folds recognize the same ligand fragments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

SITEHOUND-web: a server for ligand binding site identification in protein structures.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

Structure-based function prediction: approaches and applications.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

A novel approach to local similarity of protein binding sites substantially improves computational drug design results

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

firestar--prediction of functionally important residues using structural templates and alignment reliability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

Query3d: a new method for high-throughput analysis of functional residues in protein structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

pdbFun: mass selection and fast comparison of annotated PDB residues

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

PISCES: a protein sequence culling server

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

THEMATICS: a simple computational predictor of enzyme function from structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

Protein clefts in molecular recognition and function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

Amino acid preferences at protein binding sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3434446

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

6 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S17

Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S17

Identification of protein binding surfaces using surface triplet propensities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S17

SuperStar: a knowledge-based approach for identifying interaction sites in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S17

Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S17

The prediction and characterization of metal binding sites in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S17

PQS: a protein quaternary structure file server

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S17

Network Analysis of Protein Structures Identifies Functional Residues

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-S4-S17

10.1186/1471-2105-13-S4-S17

21 January 2018

Identifiers

DOI

1 reference

journals/bmcbi/BianchiGHA12

31 July 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

31 July 2017

1 reference

PubMed ID

22536963