Binding Kinetics in Drug Discovery

A spatiotemporal characterization of the effect of p53 phosphorylation on its interaction with MDM2

(2015) Karim M ElSawy et al.   CELL CYCLE

Insights from Fragment Hit Binding Assays by Molecular Simulations

(2015) Noelia Ferruz et al.   Journal of Chemical Information and Modeling

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

(2015) Nuria Plattner et al.   Nature Communications

Cloud computing approaches for prediction of ligand binding poses and pathways

(2015) Morgan Lawrenz et al.   Scientific Reports

Kinetic Characterization of Fragment Binding in AmpC β-Lactamase by High-Throughput Molecular Simulations

(2014) P. Bisignano et al.   Journal of Chemical Information and Modeling

Agonists for the Adenosine A1 Receptor with Tunable Residence Time. A Case for Nonribose 4-Amino-6-aryl-5-cyano-2-thiopyrimidines

(2014) Julien Louvel et al.   JOURNAL OF MEDICINAL CHEMISTRY

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

(2014) Jeffrey Comer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The in vitro and in vivo profile of aclidinium bromide in comparison with glycopyrronium bromide

(2014) Amadeu Gavaldà et al.   PULMONARY PHARMACOLOGY & THERAPEUTICS

Fluorescent approaches for understanding interactions of ligands with G protein coupled receptors

(2013) Rajashri Sridharan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

On the origin of the stereoselective affinity of Nutlin-3 geometrical isomers for the MDM2 protein

(2013) Karim ElSawy et al.   CELL CYCLE

On the interaction mechanisms of a p53 peptide and nutlin with the MDM2 and MDMX proteins: A Brownian dynamics study

(2013) Karim ElSawy et al.   CELL CYCLE

Molecular determinants of drug–receptor binding kinetics

(2013) Albert C. Pan et al.   DRUG DISCOVERY TODAY

Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules

(2013) Frank Noé et al.   JOURNAL OF CHEMICAL PHYSICS

Monte Carlo Free Ligand Diffusion with Markov State Model Analysis and Absolute Binding Free Energy Calculations

(2013) Ryoji Takahashi et al.   Journal of Chemical Theory and Computation

Free energy landscape for the binding process of Huperzine A to acetylcholinesterase

(2013) Fang Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ligand–receptor interaction platforms and their applications for drug discovery

(2012) Ye Fang   Expert Opinion on Drug Discovery

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Structure and dynamics of the M3 muscarinic acetylcholine receptor

(2012) Andrew C. Kruse et al.   NATURE

Determination of drug–receptor residence times by radioligand binding and functional assays: experimental strategies and physiological relevance

(2012) Georges Vauquelin   MedChemComm

Impact of enzyme concentration and residence time on apparent activity recovery in jump dilution analysis

(2011) Robert A. Copeland et al.   ANALYTICAL BIOCHEMISTRY

Optimized Potential of Mean Force Calculations for Standard Binding Free Energies

(2011) Ignasi Buch et al.   Journal of Chemical Theory and Computation

Characterization of the Ligand Receptor Encounter Complex and Its Potential for in Silico Kinetics-Based Drug Development

(2011) Karim M. ElSawy et al.   Journal of Chemical Theory and Computation

Molecular mechanical study of halogen bonding in drug discovery

(2011) Mahmoud A. A. Ibrahim   JOURNAL OF COMPUTATIONAL CHEMISTRY

Shielded Hydrogen Bonds as Structural Determinants of Binding Kinetics: Application in Drug Design

(2011) Peter Schmidtke et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How Does a Drug Molecule Find Its Target Binding Site?

(2011) Yibing Shan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Pathway and mechanism of drug binding to G-protein-coupled receptors

(2011) Ron O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

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

Drug–target residence time: critical information for lead optimization

(2010) Hao Lu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

A Slow, Tight Binding Inhibitor of InhA, the Enoyl-Acyl Carrier Protein Reductase fromMycobacterium tuberculosis

(2010) Sylvia R. Luckner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

(2010) I. Buch et al.   Journal of Chemical Information and Modeling

Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models

(2010) Gregory R. Bowman et al.   Journal of Chemical Theory and Computation

UDP-(5F)-GlcNAc Acts as a Slow-Binding Inhibitor of MshA, a Retaining Glycosyltransferase

(2010) Patrick A. Frantom et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

(2010) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Biochemical characterization of GSK1070916, a potent and selective inhibitor of Aurora B and Aurora C kinases with an extremely long residence time1

(2009) Kelly Anderson et al.   BIOCHEMICAL JOURNAL

Adaptive Seeding: A New Method for Simulating Biologically Relevant Timescales

(2009) Gregory R. Bowman et al.   BIOPHYSICAL JOURNAL

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations

(2009) Fabio Pietrucci et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Calculation of protein-ligand binding free energy by using a polarizable potential

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