On the Role of Physics and Evolution in Dictating Protein Structure and Function

APoc: large-scale identification of similar protein pockets

(2013) Mu Gao et al.   BIOINFORMATICS

Interplay of physics and evolution in the likely origin of protein biochemical function

(2013) Jeffrey Skolnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins

(2013) Mu Gao et al.   PLoS Computational Biology

Structural Insights into the Molecular Basis of the Ligand Promiscuity

(2012) Noé Sturm et al.   Journal of Chemical Information and Modeling

Catalytic Versatility and Backups in Enzyme Active Sites: The Case of Serum Paraoxonase 1

(2012) Moshe Ben-David et al.   JOURNAL OF MOLECULAR BIOLOGY

Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures

(2012) Jeffrey Skolnick et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation

(2012) M. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

(2012) O. Khersonsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of Chemistry versus Substrate Binding in Recruiting Promiscuous Enzyme Functions

(2011) Olga Khersonsky et al.   BIOCHEMISTRY

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function

(2011) Michal Brylinski et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

New benchmark metrics for protein-protein docking methods

(2011) Mu Gao et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Template-based protein structure modeling using TASSERVMT

(2011) Hongyi Zhou et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

(2010) Olga Khersonsky and Dan S. Tawfik   Annual Review of Biochemistry

iAlign: a method for the structural comparison of protein–protein interfaces

(2010) Mu Gao et al.   BIOINFORMATICS

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

TASSER_WT: A Protein Structure Prediction Algorithm with Accurate Predicted Contact Restraints for Difficult Protein Targets

(2010) Seung Yup Lee et al.   BIOPHYSICAL JOURNAL

Phage display: Concept, innovations, applications and future

(2010) Jyoti Pande et al.   BIOTECHNOLOGY ADVANCES

Messy biology and the origins of evolutionary innovations

(2010) Dan S Tawfik   Nature Chemical Biology

PROMISCUOUS: a database for network-based drug-repositioning

(2010) J. von Eichborn et al.   NUCLEIC ACIDS RESEARCH

Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected

(2010) M. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Rayan Chikhi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(2009) Shashi Pandit et al.   BMC BIOINFORMATICS

T3DB: a comprehensively annotated database of common toxins and their targets

(2009) Emilia Lim et al.   NUCLEIC ACIDS RESEARCH

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming

(2009) Srayanta Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Structural relationships among proteins with different global topologies and their implications for function annotation strategies

(2009) D. Petrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The continuity of protein structure space is an intrinsic property of proteins

(2009) J. Skolnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cofactor binding and enzymatic activity in an unevolved superfamily ofde novodesigned 4-helix bundle proteins

(2009) Shona C. Patel et al.   PROTEIN SCIENCE

Comparison of structure-based and threading-based approaches to protein functional annotation

(2009) Michal Brylinski et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2008) R. Najmanovich et al.   BIOINFORMATICS

Optimal contact map alignment of protein-protein interfaces

(2008) V. Pulim et al.   BIOINFORMATICS

Statistics of Random Protein Superpositions: p-Values for Pairwise Structure Alignment

(2008) James O. Wrabl et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast procedure for reconstruction of full-atom protein models from reduced representations

(2008) Piotr Rotkiewicz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Alignment of Non-Covalent Interactions at Protein-Protein Interfaces

(2008) Hongbo Zhu et al.   PLoS One

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

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

(2008) Ryoichi Minai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein–protein interaction and quaternary structure

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