The application of quantum mechanics in structure-based drug design

Calculations on Noncovalent Interactions and Databases of Benchmark Interaction Energies

(2012) Pavel Hobza   ACCOUNTS OF CHEMICAL RESEARCH

On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds

(2012) Michal Kolář et al.   Journal of Chemical Theory and Computation

Binding Affinity Prediction for Ligands and Receptors Forming Tautomers and Ionization Species: Inhibition of Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MK2)

(2012) Senthil Natesan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Inactivation of Ovine Cyclooxygenase-1 by Bromoaspirin and Aspirin: A Quantum Chemistry Description

(2012) Ito L. Barroso-Neto et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring chemistry with the fragment molecular orbital method

(2012) Dmitri G. Fedorov et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

To measure is to know: an approach to CADD performance metrics

(2011) Deborah Loughney et al.   DRUG DISCOVERY TODAY

Physics-based scoring of protein–ligand interactions: explicit polarizability, quantum mechanics and free energies

(2011) Richard A Bryce   Future Medicinal Chemistry

Robust Scoring Functions for Protein–Ligand Interactions with Quantum Chemical Charge Models

(2011) Jui-Chih Wang et al.   Journal of Chemical Information and Modeling

Communication: Quantum polarized fluctuating charge model: A practical method to include ligand polarizability in biomolecular simulations

(2011) S. Roy Kimura et al.   JOURNAL OF CHEMICAL PHYSICS

Density-functional approaches to noncovalent interactions: A comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals

(2011) Lori A. Burns et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamic Precision for Electron Repulsion Integral Evaluation on Graphical Processing Units (GPUs)

(2011) Nathan Luehr et al.   Journal of Chemical Theory and Computation

Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods

(2011) Jan Řezáč et al.   Journal of Chemical Theory and Computation

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry

(2011) Zheng Fu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain

(2011) Victor M. Anisimov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computer-aided molecular design under the SWOTlight

(2011) Darren V. S. Green et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A QM/MM study of the binding of RAPTA ligands to cathepsin B

(2011) Antonella Ciancetta et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors

(2011) Petr Dobeš et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1

(2011) Victor M. Anisimov et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protein–Ligand Interaction Energies with Dispersion Corrected Density Functional Theory and High-Level Wave Function Based Methods

(2011) Jens Antony et al.   JOURNAL OF PHYSICAL CHEMISTRY A

A Simple QM/MM Approach for Capturing Polarization Effects in Protein−Ligand Binding Free Energy Calculations

(2011) Frank R. Beierlein et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accounting for non-optimal interactions in molecular recognition: a study of ion–π complexes using a QM/MM model with a dipole-polarisable MM region

(2011) Qiantao Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method

(2011) Michael P Mazanetz et al.   Journal of Cheminformatics

Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories

(2010) Kevin E. Riley et al.   CHEMICAL REVIEWS

High-Throughput Virtual Screening Using Quantum Mechanical Probes: Discovery of Selective Kinase Inhibitors

(2010) Ting Zhou et al.   ChemMedChem

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

Quantum Mechanical Methods for Drug Design

(2010) Ting Zhou et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations

(2010) D. J. Cole et al.   EPL

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

A New Empirical Correction to the AM1 Method for Macromolecular Complexes

(2010) Michael E. Foster et al.   Journal of Chemical Theory and Computation

Mixed Quantum Mechanics/Molecular Mechanics Scoring Function To Predict Protein−Ligand Binding Affinity

(2010) Seth A. Hayik et al.   Journal of Chemical Theory and Computation

A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent-dependent reactions

(2010) Kenji Hori et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

An evaluation of the GLYCAM06 and MM3 force fields, and the PM3-D* molecular orbital method for modelling prototype carbohydrate–aromatic interactions

(2010) Anitha Ramraj et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

GPU-accelerated molecular modeling coming of age

(2010) John E. Stone et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations

(2010) Christopher B. Barnett et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands

(2010) Jindřich Fanfrlík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Rigorous Free Energy Calculations in Structure-Based Drug Design

(2010) Julien Michel  et al.   Molecular Informatics

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Assessment of QM/MM Scoring Functions for Molecular Docking to HIV-1 Protease

(2009) Pedro Fong et al.   Journal of Chemical Information and Modeling

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

Improved Hydrogen Bonding at the NDDO-Type Semiempirical Quantum Mechanical/Molecular Mechanical Interface

(2009) Qiantao Wang et al.   Journal of Chemical Theory and Computation

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

(2009) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

(2009) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods

(2009) Martin Korth et al.   Journal of Chemical Theory and Computation

Extension of QM/MM docking and its applications to metalloproteins

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

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions

(2009) Aleksandr V. Marenich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accelerating Density Functional Calculations with Graphics Processing Unit

(2008) Koji Yasuda   Journal of Chemical Theory and Computation

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation

(2008) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

Toward accurate relative energy predictions of the bioactive conformation of drugs

(2008) Keith T. Butler et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Assessing the Role of Polarization in Docking

(2008) Christopher J. R. Illingworth et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Accelerating Resolution-of-the-Identity Second-Order Møller−Plesset Quantum Chemistry Calculations with Graphical Processing Units†

(2008) Leslie Vogt et al.   JOURNAL OF PHYSICAL CHEMISTRY A

OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application

(2008) Tell Tuttle et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS