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List of works by Jan Řezáč

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

scientific article published on July 2011
Halogen bond tunability I: the effects of aromatic fluorine substitution on the strengths of halogen-bonding interactions involving chlorine, bromine, and iodine

scientific article published on 04 March 2011
Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods

scientific article published on 22 December 2011
Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes

scientific article published on 26 May 2009
A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods

article by Martin Korth et al published 12 January 2010 in Journal of Chemical Theory and Computation
Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the “Gold Standard,” CCSD(T) at the Complete Basis Set Limit?

scientific article published on April 4, 2013
Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules

Benzene Dimer: High-Level Wave Function and Density Functional Theory Calculations

scientific article published on November 2008
The accuracy of quantum chemical methods for large noncovalent complexes.

scientific article published on August 2013
Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set.

scientific article
Halogen bond tunability II: the varying roles of electrostatic and dispersion contributions to attraction in halogen bonds.

scientific article
Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples

scholarly article by Jan Řezáč et al published 2008 in Collection of Czechoslovak Chemical Communications
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

article
Cuby: An integrative framework for computational chemistry

scientific article published on February 3, 2016
Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications

scientific article published on March 4, 2016
Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems

article
Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries

article by Jan Řezáč et al published 8 November 2011 in Journal of Chemical Theory and Computation
Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field

scientific article published on 13 March 2008
Extrapolation and Scaling of the DFT-SAPT Interaction Energies toward the Basis Set Limit

scientific article published on February 10, 2011
Modulation of aldose reductase inhibition by halogen bond tuning

scientific article
Design of HIV protease inhibitors based on inorganic polyhedral metallacarboranes

scientific article
Assessment of the performance of MP2 and MP2 variants for the treatment of noncovalent interactions.

scientific article published on 18 April 2012
Surface residues dynamically organize water bridges to enhance electron transfer between proteins.

scientific article
The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design

scientific article published on 13 August 2013
Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, While the Empirical Potential Fails

scientific article published on 16 June 2011
A halogen-bonding correction for the semiempirical PM6 method

MP2.X: a generalized MP2.5 method that produces improved binding energies with smaller basis sets

article published in 2011
Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.

scientific article published in February 2011
MP2.5 and MP2.X: approaching CCSD(T) quality description of noncovalent interaction at the cost of a single CCSD iteration

scientific article published on 11 January 2013
Spin-component scaled coupled-clusters singles and doubles optimized towards calculation of noncovalent interactions

On the role of charge transfer in halogen bonding

scientific article published on 8 December 2016
QM/MM calculations reveal the different nature of the interaction of two carborane-based sulfamide inhibitors of human carbonic anhydrase II.

scientific article
Quantum Mechanics-Based Scoring Rationalizes the Irreversible Inactivation of Parasitic Schistosoma mansoni Cysteine Peptidase by Vinyl Sulfone Inhibitors

scientific article published on 21 November 2013
Quantum effects in biological electron transfer

Introduction: Noncovalent Interactions

article published in 2016
Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods

scientific article published in July 2015
On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions

Malonate-based inhibitors of mammalian serine racemase: kinetic characterization and structure-based computational study.

scientific article published on 16 October 2014
Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine (GFA) tripeptide: experiment and theory

scientific article published in January 2008
Robust and Efficient Constrained DFT Molecular Dynamics Approach for Biochemical Modeling

scientific article published on 10 January 2012
Stretched DNA investigated using molecular-dynamics and quantum-mechanical calculations.

scientific article
Multilevel Fragment-Based Approach (MFBA): A Novel Hybrid Computational Method for the Study of Large Molecules

SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses.

scientific article
Macrocycle Conformational Sampling by DFT-D3/COSMO-RS Methodology.

scientific article published on 28 November 2017
The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein-ligand interactions and implicit COSMO solvation

scientific article published on 29 January 2016
CCSD[T] Describes Noncovalent Interactions Better than the CCSD(T), CCSD(TQ), and CCSDT Methods

scientific article published on 16 November 2012
Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes.

scientific article published on 5 September 2016
Robust, Basis-Set Independent Method for the Evaluation of Charge-Transfer Energy in Noncovalent Complexes

article published in 2015
Benzene Dimer: Dynamic Structure and Thermodynamics Derived from On-the-Fly ab initio DFT-D Molecular Dynamic Simulations

article by Jan Řezáč & Pavel Hobza published 11 November 2008 in Journal of Chemical Theory and Computation
Ab Initio Quantum Mechanical Description of Noncovalent Interactions at Its Limits: Approaching the Experimental Dissociation Energy of the HF Dimer

scientific article published on June 25, 2014

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