(Q35123314)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

title

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0. (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

Daisuke Kihara

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

author name string

Xiaolei Zhu

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

language of work or name

English

0 references

publication date

29 October 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

volume

31

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

page(s)

707-713

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json

GalaxySite: ligand-binding-site prediction by using molecular docking

22 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

APoc: large-scale identification of similar protein pockets

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Binding ligand prediction for proteins using partial matching of local surface patches

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Energetics-based discovery of protein-ligand interactions on a proteomic scale

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Real-time ligand binding pocket database search using local surface descriptors

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Rapid comparison of protein binding site surfaces with property encoded shape distributions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

FINDSITE: a threading-based approach to ligand homology modeling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Characterization of local geometry of protein surfaces with the visibility criterion.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Shape variation in protein binding pockets and their ligands

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

TM-align: a protein structure alignment algorithm based on the TM-score

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Finding protein targets for small biologically relevant ligands across fold space using inverse ligand binding predictions.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Detection of multiscale pockets on protein surfaces using mathematical morphology.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

The multiple common point set problem and its application to molecule binding pattern detection

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Identification of the ligand binding sites on the molecular surface of proteins

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4341070

10.1093/BIOINFORMATICS/BTU724

27 September 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json

journals/bioinformatics/ZhuXK15

22 February 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:25359888%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

PubMed publication ID

25359888

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25359888%20AND%20SRC:MED&resulttype=core&format=json