Jan Řezáč
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View article: Comparative Analysis of Quantum-Mechanical and Standard Single-Structure Protein–Ligand Scoring Functions with MD-Based Free Energy Calculations
Comparative Analysis of Quantum-Mechanical and Standard Single-Structure Protein–Ligand Scoring Functions with MD-Based Free Energy Calculations Open
Single-structure scoring functions have been considered inferior to expensive ensemble free energy methods in predicting protein-ligand affinities. We are revisiting this dogma with the recently developed semiempirical quantum-mechanical (…
View article: Benchmark of Approximate Quantum Chemical and Machine Learning Potentials for Biochemical Proton Transfer Reactions
Benchmark of Approximate Quantum Chemical and Machine Learning Potentials for Biochemical Proton Transfer Reactions Open
Proton transfer reactions are among the most common chemical transformations and are central to enzymatic catalysis and bioenergetic processes. Their mechanisms are often investigated using DFT or approximate quantum chemical methods, whos…
View article: Multiscale Computational Protocols for Accurate Residue Interactions at the Flexible Insulin–Receptor Interface
Multiscale Computational Protocols for Accurate Residue Interactions at the Flexible Insulin–Receptor Interface Open
The quantitative characterization of residue contributions to protein-protein binding across extensive flexible interfaces poses a significant challenge for biophysical computations. It is attributable to the inherent imperfections in the …
View article: Benchmark of approximate quantum chemical and machine learning potentials for biochemical proton transfer reactions
Benchmark of approximate quantum chemical and machine learning potentials for biochemical proton transfer reactions Open
Proton transfer reactions are among the most common chemical transformations and are central to enzymatic catalysis and bioenergetic processes. Their mechanisms are often investigated using DFT or approximate quantum chemical methods, whos…
View article: On-Resin Assembly of Macrocyclic Inhibitors of <i>Cryptococcus neoformans</i> May1: A Pathway to Potent Antifungal Agents
On-Resin Assembly of Macrocyclic Inhibitors of <i>Cryptococcus neoformans</i> May1: A Pathway to Potent Antifungal Agents Open
Macrocyclic inhibitors have emerged as a privileged scaffold in medicinal chemistry, offering enhanced selectivity, stability, and pharmacokinetic profiles compared to their linear counterparts. Here, we describe a novel, on-resin macrocyc…
View article: Comparative Analysis of Quantum-Mechanical and standard Single-Structure Protein-Ligand Scoring Functions with MD-Based Free Energy Calculations
Comparative Analysis of Quantum-Mechanical and standard Single-Structure Protein-Ligand Scoring Functions with MD-Based Free Energy Calculations Open
Single-structure scoring functions have been considered inferior to expensive ensemble free energy methods in predicting protein-ligand affinities. We are revisiting this dogma with the recently developed semiempirical quantum-mechanical (…
View article: PM6-ML: The Synergy of Semiempirical Quantum Chemistry and Machine Learning Transformed into a Practical Computational Method
PM6-ML: The Synergy of Semiempirical Quantum Chemistry and Machine Learning Transformed into a Practical Computational Method Open
Machine learning (ML) methods offer a promising route to the construction of universal molecular potentials with high accuracy and low computational cost. It is becoming evident that integrating physical principles into these models, or ut…
View article: Multiscale Computational Protocols for Accurate Residue Interactions at Flexible Protein–Protein Interfaces
Multiscale Computational Protocols for Accurate Residue Interactions at Flexible Protein–Protein Interfaces Open
The quantitative characterization of residue contributions to protein-protein binding across extensive flexible interfaces poses a significant challenge for biophysical computations. This is attributable to the imperfections inherent in th…
View article: PM6-ML: The Synergy of Semiempirical Quantum Chemistry and Machine Learning Transformed into a Practical Computational Method
PM6-ML: The Synergy of Semiempirical Quantum Chemistry and Machine Learning Transformed into a Practical Computational Method Open
Machine learning (ML) methods offer a promising route to the construction of universal molecular potentials with high accuracy and low computational cost. It is becoming evident that integrating physical principles into these models, or ut…
View article: Heats of formation on the way from B<sub>2</sub>H<sub>6</sub> to B<sub>20</sub>H<sub>16</sub>: thermochemical consequences of multicenter bonding in <i>ab initio</i> and DFT methods
Heats of formation on the way from B<sub>2</sub>H<sub>6</sub> to B<sub>20</sub>H<sub>16</sub>: thermochemical consequences of multicenter bonding in <i>ab initio</i> and DFT methods Open
The objective of this study is to evaluate the effectiveness of various computational methods in reproducing the experimental heats of formation of boron hydrides using the atomization energy approach.
View article: PM6-ML: The Synergy of Semiempirical Quantum Chemistry and Machine Learning Transformed into a Practical Computational Method
PM6-ML: The Synergy of Semiempirical Quantum Chemistry and Machine Learning Transformed into a Practical Computational Method Open
Machine learning (ML) methods offer a promising route to the construction of universal molecular potentials with high accuracy and low computational cost. It is becoming evident that integrating physical principles into these models, or ut…
View article: PM6-ML: The Synergy of Semiempirical Quantum Chemistry and Machine Learning Transformed into a Practical Computational Method
PM6-ML: The Synergy of Semiempirical Quantum Chemistry and Machine Learning Transformed into a Practical Computational Method Open
Machine learning (ML) methods offer a promising route to the construction of universal molecular potentials with high accuracy and low computational cost. It is becoming evident that integrating physical principles into these models, or ut…
View article: Extensive targeting of chemical space at the prime side of ketoamide inhibitors of rhomboid proteases by branched substituents empowers their selectivity and potency
Extensive targeting of chemical space at the prime side of ketoamide inhibitors of rhomboid proteases by branched substituents empowers their selectivity and potency Open
Rhomboid intramembrane serine proteases have been implicated in several pathologies, and emerge as attractive pharmacological target candidates. The most potent and selective rhomboid inhibitors available to date are peptidyl α-ketoamides,…
View article: Working with benchmark datasets in the Cuby framework
Working with benchmark datasets in the Cuby framework Open
The development and benchmarking of computational chemistry methods rely on comparison with benchmark data. More and larger benchmark datasets are becoming available, and working efficiently with them is a necessity. The Cuby framework pro…
View article: Working with benchmark datasets in the Cuby framework
Working with benchmark datasets in the Cuby framework Open
The development and benchmarking of computational chemistry methods relies on comparison with benchmark data. More and larger benchmark datasets are becoming available, and working efficiently with them is a necessity. The Cuby framework p…
View article: SQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein–ligand binding affinity predictions in minutes
SQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein–ligand binding affinity predictions in minutes Open
Accurate estimation of protein–ligand binding affinity is the cornerstone of computer-aided drug design. We present a universal physics-based scoring function, named SQM2.20, addressing key terms of binding free energy using semiempirical …
View article: Extensive Targeting of Chemical Space at the Prime Side of Ketoamide Inhibitors of Rhomboid Proteases by Branched Substituents Empowers Their Selectivity and Potency
Extensive Targeting of Chemical Space at the Prime Side of Ketoamide Inhibitors of Rhomboid Proteases by Branched Substituents Empowers Their Selectivity and Potency Open
View article: SQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein–ligand binding affinity predictions in minutes
SQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein–ligand binding affinity predictions in minutes Open
Accurate estimation of protein–ligand binding affinity is the cornerstone of computer-aided drug design. We present a universal physics-based scoring function, named SQM2.20, addressing key terms of binding free energy using semiempirical …
View article: On the role of charge transfer in many-body non-covalent interactions
On the role of charge transfer in many-body non-covalent interactions Open
Charge transfer is one of the mechanisms involved in non-covalent interactions. In molecular dimers, its contribution to pairwise interaction energies has been studied extensively using a variety of interaction energy decomposition schemes…
View article: On the role of charge transfer in many-body non-covalent interactions
On the role of charge transfer in many-body non-covalent interactions Open
Charge transfer is one of the mechanisms involved in non-covalent interactions. In molecular dimers, its contribution to pairwise interaction energies has been studied extensively using a variety of interaction energy decomposition schemes…
View article: On the role of charge transfer in many-body non-covalent interactions
On the role of charge transfer in many-body non-covalent interactions Open
Charge transfer is one of the mechanisms involved in non-covalent interactions. In molecular dimers, its contribution to the pairwise interaction energies has been studied extensively using a variety of interaction energy decomposition sch…
View article: Erratum: “DFTB+, a software package for efficient approximate density functional theory based atomistic simulations” [J. Chem. Phys. 152, 124101 (2020)]
Erratum: “DFTB+, a software package for efficient approximate density functional theory based atomistic simulations” [J. Chem. Phys. 152, 124101 (2020)] Open
The implementation of the GPU support in DFTB+, as described in Sec. III C of the original publication,1 was developed based on a previous unpublished implementation by Jacek Jakowski. In order to acknowledge his work on this first impleme…
View article: Non-Covalent Interactions Atlas Benchmark Data Sets 4: σ-Hole Interactions
Non-Covalent Interactions Atlas Benchmark Data Sets 4: σ-Hole Interactions Open
The SH250×10 dataset presented here extends the Non-Covalent Interactions Atlas database (www.nciatlas.org) to complexes bound by σ-hole interactions – halogen, chalcogen and pnictogen bonds. It comprises 250 complexes where Cl, Br, I, S, …
View article: Non-Covalent Interactions Atlas Benchmark Data Sets 5: London Dispersion in an Extended Chemical Space
Non-Covalent Interactions Atlas Benchmark Data Sets 5: London Dispersion in an Extended Chemical Space Open
The Non-Covalent Interactions Atlas (www.nciatlas.org) has been extended with two data sets of benchmark interaction energies in complexes dominated by London dispersion. The D1200 data set of equilibrium geometries provides a thorough sam…
View article: Spin-component-scaled and dispersion-corrected second-order Møller-Plesset perturbation theory: A path toward chemical accuracy
Spin-component-scaled and dispersion-corrected second-order Møller-Plesset perturbation theory: A path toward chemical accuracy Open
Second-order Møller-Plesset perturbation theory (MP2) provides a valuable alternative to density functional theory for modeing problems in organic and biological chemistry. However, MP2 suffers from known lim- itations in the description o…
View article: Spin-component-scaled and dispersion-corrected second-order Møller-Plesset perturbation theory: A path toward chemical accuracy
Spin-component-scaled and dispersion-corrected second-order Møller-Plesset perturbation theory: A path toward chemical accuracy Open
Second-order Møller-Plesset perturbation theory (MP2) provides a valuable alternative to density functional theory for modeing problems in organic and biological chemistry. However, MP2 suffers from known lim- itations in the description o…
View article: CCDC 1459072: Experimental Crystal Structure Determination
CCDC 1459072: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1459071: Experimental Crystal Structure Determination
CCDC 1459071: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: Conformational energies and equilibria of cyclic dinucleotides<i>in vacuo</i>and in solution: computational chemistry<i>vs.</i>NMR experiments
Conformational energies and equilibria of cyclic dinucleotides<i>in vacuo</i>and in solution: computational chemistry<i>vs.</i>NMR experiments Open
Computational “error bars” for modelling cyclic dinucleotides – NMR experimentvs.quantum mechanics and molecular dynamics.
View article: Non-Covalent Interactions Atlas Benchmark Data Sets 3: Repulsive Contacts
Non-Covalent Interactions Atlas Benchmark Data Sets 3: Repulsive Contacts Open
The new R739×5 data set from the Non-Covalent Interactions Atlas series (www.nciatlas.org) focuses on repulsive contacts in molecular complexes, covering organic molecules, sulfur, phosphorus, halogens and noble gases. Information on the r…