Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain

Evidence for Substrate Binding-Induced Zwitterion Formation in the Catalytic Cys-His Dyad of the SARS-CoV Main Protease

(2014) Alexander Paasche et al.   BIOCHEMISTRY

The Protonation State of Catalytic Residues in the Resting State of KasA Revisited: Detailed Mechanism for the Activation of KasA by Its Own Substrate

(2014) Wook Lee et al.   BIOCHEMISTRY

Reaction Pathway and Free Energy Profile for Papain-Catalyzed Hydrolysis of N-Acetyl-Phe-Gly 4-Nitroanilide

(2013) Donghui Wei et al.   BIOCHEMISTRY

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Benchmark Study for the Cysteine–Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches

(2013) Alexander Paasche et al.   Journal of Chemical Theory and Computation

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

(2013) Chuan Li et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Mechanism of the irreversible inhibition of human cyclooxygenase-1 by aspirin as predicted by QM/MM calculations

(2013) L. Tóth et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Performance of M06, M06-2X, and M06-HF Density Functionals for Conformationally Flexible Anionic Clusters: M06 Functionals Perform Better than B3LYP for a Model System with Dispersion and Ionic Hydrogen-Bonding Interactions

(2013) Martin Walker et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Clarification on the Decarboxylation Mechanism in KasA Based on the Protonation State of Key Residues in the Acyl-Enzyme State

(2013) Wook Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the method-dependence of transition state asynchronicity in Diels–Alder reactions

(2013) Mats Linder et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives

(2012) Mateusz Marianski et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: Dispersion, induction, and basis set superposition error

(2012) Dipankar Roy et al.   JOURNAL OF CHEMICAL PHYSICS

Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions

(2012) Richard Lonsdale et al.   Journal of Chemical Theory and Computation

DelPhi: a comprehensive suite for DelPhi software and associated resources

(2012) Lin Li et al.   BMC Biophysics

Elucidation of the Protonation States of the Catalytic Residues inmtKasA: Implications for Inhibitor Design

(2011) Wook Lee et al.   BIOCHEMISTRY

Dispersion Interactions with Density-Functional Theory: Benchmarking Semiempirical and Interatomic Pairwise Corrected Density Functionals

(2011) Noa Marom et al.   Journal of Chemical Theory and Computation

Density Functional Theory for Reaction Energies: Test of Meta and Hybrid Meta Functionals, Range-Separated Functionals, and Other High-Performance Functionals

(2011) Yan Zhao et al.   Journal of Chemical Theory and Computation

Applications and validations of the Minnesota density functionals

(2010) Yan Zhao et al.   CHEMICAL PHYSICS LETTERS

Computational Evidence for the Catalytic Mechanism of Caspase-7. A DFT Investigation

(2010) Gian Pietro Miscione et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Active Site Cysteine Is Protonated in the PAD4 Michaelis Complex: Evidence from Born−Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations

(2009) Zhihong Ke et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Challenging a paradigm: Theoretical calculations of the protonation state of the Cys25-His159 catalytic diad in free papain

(2009) Michael Shokhen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

On the Origin of the Stabilization of the Zwitterionic Resting State of Cysteine Proteases: A Theoretical Study

(2008) Milena Mladenovic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections

(2008) Jeng-Da Chai et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS