Fully ab initio protein-ligand interaction energies with dispersion corrected density functional theory

Difficulties in applying pure Kohn–Sham density functional theory electronic structure methods to protein molecules

(2012) Elias Rudberg   JOURNAL OF PHYSICS-CONDENSED MATTER

Performance of dispersion-corrected density functional theory for the interactions in ionic liquids

(2012) Stefan Grimme et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Fragmentation Methods: A Route to Accurate Calculations on Large Systems

(2011) Mark S. Gordon et al.   CHEMICAL REVIEWS

Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non-Covalent Interactions

(2011) Lars Goerigk et al.   CHEMPHYSCHEM

Investigation of the Differences in Activity between Hydroxycycloalkyl N1 Substituted Pyrazole Derivatives As Inhibitors of B-Raf Kinase by Using Docking, Molecular Dynamics, QM/MM, and Fragment-BasedDe NovoDesign: Study of Binding Mode of Diastereomer Compounds

(2011) Julio Caballero et al.   Journal of Chemical Information and Modeling

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

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

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

S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures

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

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

Energy Decomposition Analysis in Solution Based on the Fragment Molecular Orbital Method

(2011) Dmitri G. Fedorov et al.   JOURNAL OF PHYSICAL CHEMISTRY A

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

Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, While the Empirical Potential Fails

(2011) Petr Dobeš et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics

(2011) Ivan S. Ufimtsev et al.   Journal of Physical Chemistry Letters

Higher-order correlated calculations based on fragment molecular orbital scheme

(2011) Yuji Mochizuki et al.   THEORETICAL CHEMISTRY ACCOUNTS

Wavefunction methods for noncovalent interactions

(2011) Edward G. Hohenstein et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Density functional theory with London dispersion corrections

(2011) Stefan Grimme   Wiley Interdisciplinary Reviews-Computational Molecular Science

Frontiers in electronic structure theory

(2010) C. David Sherrill   JOURNAL OF CHEMICAL PHYSICS

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

Ligand Affinities Estimated by Quantum Chemical Calculations

(2010) Pär Söderhjelm et al.   Journal of Chemical Theory and Computation

Kohn−Sham Density Functional Theory Electronic Structure Calculations with Linearly Scaling Computational Time and Memory Usage

(2010) Elias Rudberg et al.   Journal of Chemical Theory and Computation

Challenges and advances in computational docking: 2009 in review

(2010) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

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

Estimates of ligand-binding affinities supported by quantum mechanical methods

(2010) Pär Söderhjelm et al.   Interdisciplinary Sciences-Computational Life Sciences

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

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

QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena?

(2009) M. Paul Gleeson 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

Quantum mechanical scoring for protein docking

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

Insights into docking and scoring neuronal α4β2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations

(2009) Jacopo Sgrignani et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Extension of QM/MM docking and its applications to metalloproteins

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

Cooperativity in noncovalent interactions of biologically relevant molecules

(2009) Jens Antony et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A fast method of large-scale serial semiempirical calculations of docking complexes

(2009) N. A. Anikin et al.   RUSSIAN CHEMICAL BULLETIN

A method and program for mass quantum chemical calculations of protein—ligand docking complexes

(2009) N. A. Anikin et al.   RUSSIAN CHEMICAL BULLETIN

The augmented Roothaan–Hall method for optimizing Hartree–Fock and Kohn–Sham density matrices

(2008) Stinne Høst et al.   JOURNAL OF CHEMICAL PHYSICS

QM/QM docking method based on the variational finite localized molecular orbital approximation

(2008) Victor M. Anisimov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Interpretation of Protein/Ligand Crystal Structure using QM/MM Calculations: Case of HIV-1 Protease/Metallacarborane Complex

(2008) Jindřich Fanfrlík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evaluation of methods to cap molecular fragments in calculating energies of interaction in avian pancreatic polypeptide

(2007) Marcus P. D. Hatfield et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY