4.3 Article

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

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

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

Kota Kasahara et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

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

Heng Li et al.

BIOINFORMATICS (2010)

Article Chemistry, Medicinal

Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein-Ligand Binding Sites

Nathanael Weill et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)

Article Computer Science, Artificial Intelligence

Multi-sorting algorithm for finding pairs of similar short substrings from large-scale string data

Takeaki Uno

KNOWLEDGE AND INFORMATION SYSTEMS (2010)

Article Biochemistry & Molecular Biology

Detection of multiscale pockets on protein surfaces using mathematical morphology

Takeshi Kawabata

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

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

Rayan Chikhi et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Biochemical Research Methods

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

Xue-Wen Chen et al.

BIOINFORMATICS (2009)

Article Multidisciplinary Sciences

Fast screening of protein surfaces using geometric invariant fingerprints

Shuangye Yin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biochemistry & Molecular Biology

Comprehensive Structural Classification of Ligand-Binding Motifs in Proteins

Akira R. Kinjo et al.

STRUCTURE (2009)

Article Biochemical Research Methods

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

John A. Capra et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Biochemistry & Molecular Biology

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

Claire Schalon et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

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

Ryoichi Minai et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

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

Margarita Malakhova et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Prediction of transition metal-binding sites from apo protein structures

Mariana Babor et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)

Article Biochemical Research Methods

Moment invariants as shape recognition technique for comparing protein binding sites

Ingolf Sommer et al.

BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

Elucidation of the active conformation of the APS-kinase domain of human PAPS synthetase 1

Nikolina Sekulic et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Review Biochemistry & Molecular Biology

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

Zenon Grabarek

JOURNAL OF MOLECULAR BIOLOGY (2006)

Article Biochemistry & Molecular Biology

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

ND Gold et al.

JOURNAL OF MOLECULAR BIOLOGY (2006)

Article Biochemistry & Molecular Biology

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

B Wang et al.

FEBS LETTERS (2006)

Article Biochemical Research Methods

Pocketome via comprehensive identification and classification of ligand binding envelopes

JH An et al.

MOLECULAR & CELLULAR PROTEOMICS (2005)

Article Biochemistry & Molecular Biology

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

HR Gentry et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2005)

Article Biochemistry & Molecular Biology

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

Y Zhang et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

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

YW Yan et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Recognition of functional sites in protein structures

A Shulman-Peleg et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Article Biochemistry & Molecular Biology

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

IY Park et al.

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY (2004)

Article Biochemistry & Molecular Biology

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

M Jambon et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)

Article Biochemistry & Molecular Biology

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

B Ahvazi et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2003)

Article Biochemistry & Molecular Biology

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

M Kato et al.

MOLECULAR CELL (2003)

Article Biochemistry & Molecular Biology

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

S Schmitt et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Article Biochemistry & Molecular Biology

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

B Dalhus et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Article Biochemistry & Molecular Biology

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

KKS Ng et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2002)

Article Biochemistry & Molecular Biology

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

RT Bossi et al.

BIOCHEMISTRY (2002)

Review Biochemistry & Molecular Biology

Sequence-structure analysis of FAD-containing proteins

O Dym et al.

PROTEIN SCIENCE (2001)

Article Biochemistry & Molecular Biology

Fast prediction and visualization of protein binding pockets with PASS

GP Brady et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2000)

Article Biochemistry & Molecular Biology

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

H Pan et al.

STRUCTURE (2000)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)