Enhanced molecular dynamics sampling of drug target conformations

Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl cis – trans isomerases

(2015) Safieh Tork Ladani et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics

(2015) Urmi Doshi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Molecular dynamics in drug design

(2015) Hongtao Zhao et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent

(2014) Urmi Doshi et al.   Journal of Physical Chemistry Letters

Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug Design

(2013) Mulpuri Nagaraju et al.   Journal of Chemical Information and Modeling

An Overview of Cyclophilins in Human Cancers

(2013) J Lee et al.   JOURNAL OF INTERNATIONAL MEDICAL RESEARCH

Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions

(2012) Urmi Doshi et al.   Journal of Chemical Theory and Computation

A family of cyclophilin-like molecular chaperones in Plasmodium falciparum

(2012) Alejandro Marín-Menéndez et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Resolving the complex role of enzyme conformational dynamics in catalytic function

(2012) U. Doshi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibacterial drug leads targeting isoprenoid biosynthesis

(2012) W. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular dynamics simulations and drug discovery

(2011) Jacob D Durrant et al.   BMC BIOLOGY

Prolyl cis/trans isomerase signalling pathways in cancer

(2011) Martin Theuerkorn et al.   CURRENT OPINION IN PHARMACOLOGY

Computational Insight into Small Molecule Inhibition of Cyclophilins

(2011) Somisetti V. Sambasivarao et al.   Journal of Chemical Information and Modeling

Studying functional dynamics in bio-molecules using accelerated molecular dynamics

(2011) Phineus R. L. Markwick et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics

(2011) Denis Bucher et al.   PLoS Computational Biology

The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors

(2011) Susanne Pfefferle et al.   PLoS Pathogens

Water’s Contribution to the Energetic Roughness from Peptide Dynamics

(2010) Quentin Johnson et al.   Journal of Chemical Theory and Computation

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations

(2010) Jeff Wereszczynski et al.   Journal of Chemical Theory and Computation

Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins

(2010) Phineus R. L. Markwick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

Isoform-Specific Inhibition of Cyclophilins

(2009) Sebastian Daum et al.   BIOCHEMISTRY

The Isomerase Active Site of Cyclophilin A Is Critical for Hepatitis C Virus Replication

(2009) Udayan Chatterji et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reoptimization of the AMBER Force Field Parameters for Peptide Bond (Omega) Torsions Using Accelerated Molecular Dynamics

(2009) Urmi Doshi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Toward a Unified Representation of Protein Structural Dynamics in Solution

(2009) Phineus R. L. Markwick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanistic Insight into the Role of Transition-State Stabilization in Cyclophilin A

(2009) Donald Hamelberg et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics

(2009) Barry J. Grant et al.   PLoS Computational Biology

A statistical analysis of the precision of reweighting-based simulations

(2008) Tongye Shen et al.   JOURNAL OF CHEMICAL PHYSICS

An integrate-over-temperature approach for enhanced sampling

(2008) Yi Qin Gao   JOURNAL OF CHEMICAL PHYSICS