Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

Classification and Annotation of the Relationship between Protein Structural Change and Ligand Binding

(2011) Takayuki Amemiya et al.   JOURNAL OF MOLECULAR BIOLOGY

Distinct Roles of Overlapping and Non-overlapping Regions of Hub Protein Interfaces in Recognition of Multiple Partners

(2011) Bhaskar Dasgupta et al.   JOURNAL OF MOLECULAR BIOLOGY

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM

(2011) Nurcan Tuncbag et al.   Nature Protocols

Structural Similarity and Classification of Protein Interaction Interfaces

(2011) Nan Zhao et al.   PLoS One

A Critical Comparative Assessment of Predictions of Protein-Binding Sites for Biologically Relevant Organic Compounds

(2011) Ke Chen et al.   STRUCTURE

Structural Comparison of F1-ATPase: Interplay among Enzyme Structures, Catalysis, and Rotations

(2011) Kei-ichi Okazaki et al.   STRUCTURE

Negative regulation by nuclear receptors: a plethora of mechanisms

(2011) Guilherme M. Santos et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Knowledge-based annotation of small molecule binding sites in proteins

(2010) Ratna R Thangudu et al.   BMC BIOINFORMATICS

Geometric Similarities of Protein–Protein Interfaces at Atomic Resolution Are Only Observed within Homologous Families: An Exhaustive Structural Classification Study

(2010) Akira R. Kinjo et al.   JOURNAL OF MOLECULAR BIOLOGY

Proteome-wide prediction of overlapping small molecule and protein binding sites using structure

(2010) Fred P. Davis   Molecular BioSystems

Protein interactions and ligand binding: From protein subfamilies to functional specificity

(2010) A. Rausell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Docking by structural similarity at protein-protein interfaces

(2010) Rohita Sinha et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures

(2010) Fred P. Davis et al.   PLoS Computational Biology

Lessons from Structural Genomics

(2009) Thomas C. Terwilliger et al.   Annual Review of Biophysics

Exploiting structural classifications for function prediction: towards a domain grammar for protein function

(2009) Benoît H Dessailly et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Is protein classification necessary? Toward alternative approaches to function annotation

(2009) Donald Petrey et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Statistical Model of Protein Sequence Similarity and Function Similarity Reveals Overly-Specific Function Predictions

(2009) Brenton Louie et al.   PLoS One

Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

(2009) Andrew C. Wallace et al.   PROTEIN SCIENCE

Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold

(2009) Ryotaro Koike et al.   PROTEIN SCIENCE

Exploring functional roles of multibinding protein interfaces

(2009) Manoj Tyagi et al.   PROTEIN SCIENCE

Comprehensive Structural Classification of Ligand-Binding Motifs in Proteins

(2009) Akira R. Kinjo et al.   STRUCTURE

Protein function prediction – the power of multiplicity

(2009) Robert Rentzsch et al.   TRENDS IN BIOTECHNOLOGY

FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies

(2009) Oliver C. Redfern et al.   PLoS Computational Biology

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

Protein function annotation by homology-based inference

(2009) Yaniv Loewenstein et al.   GENOME BIOLOGY

Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?

(2008) Ozlem Keskin et al.   CHEMICAL REVIEWS

Protein Structural Change upon Ligand Binding Correlates with Enzymatic Reaction Mechanism

(2008) Ryotaro Koike et al.   JOURNAL OF MOLECULAR BIOLOGY

Architectures and Functional Coverage of Protein–Protein Interfaces

(2008) Nurcan Tuncbag et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2008) L. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism

(2008) J. I. Yeh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein–protein interaction and quaternary structure

(2008) Joël Janin et al.   QUARTERLY REVIEWS OF BIOPHYSICS

PPiClust: EFFICIENT CLUSTERING OF 3D PROTEIN–PROTEIN INTERACTION INTERFACES

(2008) ZEYAR AUNG et al.   Journal of Bioinformatics and Computational Biology