De novo active sites for resurrected Precambrian enzymes

Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro approach to protein engineering

(2016) Y. Gumulya et al.   BIOCHEMICAL JOURNAL

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies

(2016) Nicholas Furnham et al.   JOURNAL OF MOLECULAR BIOLOGY

Catalytic Promiscuity of Ancestral Esterases and Hydroxynitrile Lyases

(2016) Titu Devamani et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evolutionary drivers of thermoadaptation in enzyme catalysis

(2016) Vy Nguyen et al.   SCIENCE

An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors

(2016) Paola Laurino et al.   PLOS BIOLOGY

The physiology and habitat of the last universal common ancestor

(2016) Madeline C. Weiss et al.   Nature Microbiology

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily

(2015) Alexandre Barrozo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

New Tricks for Old Proteins: Single Mutations in a Nonenzymatic Protein Give Rise to Various Enzymatic Activities

(2015) Yurii S. Moroz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Catalytic efficiency of designed catalytic proteins

(2014) Ivan V Korendovych et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Drug Resistance Conferred by Mutations Outside the Active Site through Alterations in the Dynamic and Structural Ensemble of HIV-1 Protease

(2014) Debra A. Ragland et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals

(2014) Antonija Kuzmanic et al.   Nature Communications

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Hyperstability and Substrate Promiscuity in Laboratory Resurrections of Precambrian β-Lactamases

(2013) Valeria A. Risso et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Precision is essential for efficient catalysis in an evolved Kemp eliminase

(2013) Rebecca Blomberg et al.   NATURE

Experimental evidence for the thermophilicity of ancestral life

(2013) S. Akanuma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Engineering a model protein cavity to catalyze the Kemp elimination

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

Iterative approach to computational enzyme design

(2012) H. K. Privett 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

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

Design of a switchable eliminase

(2011) I. V. Korendovych et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relative Role of Halogen Bonds and Hydrophobic Interactions in Inhibition of Human Protein Kinase CK2α by Tetrabromobenzotriazole and Some C(5)-Substituted Analogues

(2010) Romualda Wąsik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modulation of Buried Ionizable Groups in Proteins with Engineered Surface Charge

(2010) Angel L. Pey et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Counterdiffusion methods applied to protein crystallization

(2009) Fermín Otálora et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

Palaeotemperature trend for Precambrian life inferred from resurrected proteins

(2008) Eric A. Gaucher et al.   NATURE

High tolerance for ionizable residues in the hydrophobic interior of proteins

(2008) D. G. Isom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA