(Q46988348)

27 December 2017

title

PDB-scale analysis of known and putative ligand-binding sites with structural sketches (English)

1 reference

27 December 2017

1 reference

5

Koji Tsuda

1 reference

27 December 2017

author name string

Jun-Ichi Ito

1

1 reference

27 December 2017

Yasuo Tabei

2

1 reference

27 December 2017

Kana Shimizu

3

1 reference

27 December 2017

Kentaro Tomii

4

1 reference

27 December 2017

language of work or name

English

0 references

publication date

24 November 2011

1 reference

27 December 2017

published in

Proteins

1 reference

27 December 2017

volume

80

1 reference

27 December 2017

issue

3

1 reference

27 December 2017

page(s)

747-763

1 reference

27 December 2017

Protein structure comparison by alignment of distance matrices

cites work

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

SCOP: a structural classification of proteins database for the investigation of sequences and structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

CATH--a hierarchic classification of protein domain structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

A serine protease triad forms the catalytic centre of a triacylglycerol lipase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

21 January 2018

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Fast prediction and visualization of protein binding pockets with PASS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Pocketome via comprehensive identification and classification of ligand binding envelopes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Detection of multiscale pockets on protein surfaces using mathematical morphology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Predicting protein interaction sites from residue spatial sequence profile and evolution rate.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Sequence-based prediction of protein interaction sites with an integrative method

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Recognition of functional sites in protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Comprehensive structural classification of ligand-binding motifs in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

A simple and fuzzy method to align and compare druggable ligand-binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Fast screening of protein surfaces using geometric invariant fingerprints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Fast and accurate long-read alignment with Burrows-Wheeler transform

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

A new bioinformatic approach to detect common 3D sites in protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Improved approximation algorithms for maximum cut and satisfiability problems using semidefinite programming

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Moment invariants as shape recognition technique for comparing protein binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structural and biochemical characterization of CIB1 delineates a new family of EF-hand-containing proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Roles of calcium ions in the activation and activity of the transglutaminase 3 enzyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Modular architecture of the bacteriophage T7 primase couples RNA primer synthesis to DNA synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Molecular basis of proton motive force generation: structure of formate dehydrogenase-N

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate dehydrogenases

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Elucidation of the Active Conformation of the APS-Kinase Domain of Human PAPS Synthetase 1

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Inhibition of a mitotic motor protein: where, how, and conformational consequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

The crystal structure of the MJ0796 ATP-binding cassette. Implications for the structural consequences of ATP hydrolysis in the active site of an ABC transporter

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structural basis for diversity of the EF-hand calcium-binding proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structure of a new nucleic-acid-binding motif in eukaryotic transcriptional elongation factor TFIIS

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structural basis for allosteric substrate specificity regulation in anaerobic ribonucleotide reductases

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

The unique hydrogen bonded water in the reduced form of Clostridium pasteurianum rubredoxin and its possible role in electron transfer

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Interactions of nucleotides with fully unadenylylated glutamine synthetase from Salmonella typhimurium

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structure and mechanism of yeast RNA triphosphatase: an essential component of the mRNA capping apparatus

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Prediction of transition metal-binding sites from apo protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Sequence-structure analysis of FAD-containing proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structure of the LKB1-STRAD-MO25 complex reveals an allosteric mechanism of kinase activation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structural basis for activation of the autoinhibitory C-terminal kinase domain of p90 RSK2

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Crystal structure of D-amino acid oxidase: a case of active site mirror-image convergent evolution with flavocytochrome b2

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structure of FAD-bound L-aspartate oxidase: insight into substrate specificity and catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Structural analysis of monosaccharide recognition by rat liver mannose-binding protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Orientation of bound ligands in mannose-binding proteins. Implications for multivalent ligand recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

Identification of protein kinases by computer

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23232

21 January 2018

Identifiers

DOI

10.1002/PROT.23232

1 reference

27 December 2017

1 reference

27 December 2017