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

APoc: large-scale identification of similar protein pockets

(2013) Mu Gao et al.   BIOINFORMATICS

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

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

(2012) Sagar D Khare et al.   Nature Chemical Biology

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

Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

(2011) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

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

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

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

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

(2010) Jinrui Xu et al.   BIOINFORMATICS

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

Protein Structure Prediction by Pro-Sp3-TASSER

(2009) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

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

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

Combinatorial bounds via measure and conquer

(2008) Fedor V. Fomin et al.   ACM Transactions on Algorithms

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

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