Combining QM/MM Calculations with Classical Mining Minima to Predict Protein–Ligand Binding Free Energy

Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation

(2021) Germano Heinzelmann et al.   Scientific Reports

Computation of host–guest binding free energies with a new quantum mechanics based mining minima algorithm

(2021) Peng Xu et al.   JOURNAL OF CHEMICAL PHYSICS

Absolute Binding Free Energy Calculation and Design of a Subnanomolar Inhibitor of Phosphodiesterase-10

(2019) Zhe Li et al.   JOURNAL OF MEDICINAL CHEMISTRY

Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations

(2017) Bing Xie et al.   Journal of Chemical Theory and Computation

In Silico Prediction of Ligand Binding Energies in Multiple Therapeutic Targets and Diverse Ligand Sets—A Case Study on BACE1, TYK2, HSP90, and PERK Proteins

(2017) Elizabeth Hatcher Frush et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Incorporating QM and solvation into docking for applications to GPCR targets

(2016) Minsup Kim et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Accurate Binding Free Energy Predictions in Fragment Optimization

(2015) Thomas B. Steinbrecher et al.   Journal of Chemical Information and Modeling

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cyclin-Dependent Kinase-2 as a Target for Cancer Therapy: Progress in the Development of CDK2 Inhibitors as Anti-Cancer Agents

(2014) Tahir Chohan et al.   CURRENT MEDICINAL CHEMISTRY

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method

(2014) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Importance of Accurate Charges in Binding Affinity Calculations: A Case of Neuraminidase Series

(2013) Kichul Park et al.   BULLETIN OF THE KOREAN CHEMICAL SOCIETY

Lead identification of novel and selective TYK2 inhibitors

(2013) Jun Liang et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Accurate Calculation of Mutational Effects on the Thermodynamics of Inhibitor Binding to p38α MAP Kinase: A Combined Computational and Experimental Study

(2013) Shun Zhu et al.   Journal of Chemical Theory and Computation

Structure based design of iminohydantoin BACE1 inhibitors: Identification of an orally available, centrally active BACE1 inhibitor

(2012) Jared N. Cumming et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Perspective: Alchemical free energy calculations for drug discovery

(2012) David L. Mobley et al.   JOURNAL OF CHEMICAL PHYSICS

Partial Atomic Charges and Screened Charge Models of the Electrostatic Potential

(2012) Bo Wang et al.   Journal of Chemical Theory and Computation

Direct thrombin inhibitors

(2011) Catherine J. Lee et al.   BRITISH JOURNAL OF CLINICAL PHARMACOLOGY

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Discovery of 6-(2,4-Difluorophenoxy)-2-[3-hydroxy-1-(2-hydroxyethyl)propylamino]-8-methyl-8H-pyrido[2,3-d]pyrimidin-7-one (Pamapimod) and 6-(2,4-Difluorophenoxy)-8-methyl-2-(tetrahydro-2H-pyran-4-ylamino)pyrido[2,3-d]pyrimidin-7(8H)-one (R1487) as Orally Bioavailable and Highly Selective Inhibitors of p38α Mitogen-Activated Protein Kinase

(2011) David M. Goldstein et al.   JOURNAL OF MEDICINAL CHEMISTRY

Basis set dependence of atomic spin populations

(2010) Jordan J. Philips et al.   CHEMICAL PHYSICS LETTERS

Modeling Protein−Ligand Binding by Mining Minima

(2010) Wei Chen et al.   Journal of Chemical Theory and Computation

Correlation between Performance of QM/MM Docking and Simple Classification of Binding Sites

(2009) Jae Yoon Chung et al.   Journal of Chemical Information and Modeling

Quantum mechanical scoring for protein docking

(2009) Art E. Cho et al.   JOURNAL OF CHEMICAL PHYSICS

Extension of QM/MM docking and its applications to metalloproteins

(2009) Art E. Cho et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

More than a Simple Lipophilic Contact: A Detailed Thermodynamic Analysis of Nonbasic Residues in the S1 Pocket of Thrombin

(2009) Bernhard Baum et al.   JOURNAL OF MOLECULAR BIOLOGY