A5015675904- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- Chemical Synthesis and Analysis
- Crystallography and molecular interactions
- Enzyme function and inhibition
- Supramolecular Chemistry and Complexes
- Advanced Chemical Physics Studies
- Microbial Metabolic Engineering and Bioproduction
- Peptidase Inhibition and Analysis
- Boron Compounds in Chemistry
- Click Chemistry and Applications
- Genetics, Bioinformatics, and Biomedical Research
- RNA and protein synthesis mechanisms
- Molecular Spectroscopy and Structure
- Biochemical effects in animals
- Fluorine in Organic Chemistry
- Metabolomics and Mass Spectrometry Studies
- Insect Resistance and Genetics
- Advanced biosensing and bioanalysis techniques
- Machine Learning in Materials Science
- Heat shock proteins research
- Organic Chemistry Cycloaddition Reactions
- Enzyme Structure and Function
Masaryk University
2022
Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry
2017-2020
Palacký University Olomouc
2017-2020
Regional Centre of Advanced Technologies and Materials
2019-2020
Czech Academy of Sciences
2017
Abstract Accurate prediction of protein–ligand binding affinities is essential for hit‐to‐lead optimization and virtual screening. The reliability scoring functions can be improved by including quantum effects. Here, we demonstrate the ranking power semiempirical mechanics (SQM)/implicit solvent (COSMO) function using a challenging set 10 inhibitors to carbonic anhydrase II through Zn 2+ in active site. This new dataset consists high‐resolution (1.1–1.4 Å) crystal structures experimentally...
A macropolyhedral boron hydride anion with two counterions can form stable complexes β- and γ-cyclodextrin in the gas phase.
General and reliable description of structures energetics in protein-ligand (PL) binding using the docking/scoring methodology has until now been elusive. We address this urgent deficiency scoring functions (SFs) by systematic development corrected semiempirical quantum mechanical (SQM) methods, which correctly describe all types noncovalent interactions are fast enough to treat systems thousands atoms. Two most accurate SQM PM6-D3H4X SCC-DFTB3-D3H4X, coupled with conductor-like screening...
Abstract This paper describes the excellent performance of a newly developed scoring function (SF), based on semiempirical QM (SQM) PM6‐D3H4X method combined with conductor‐like screening implicit solvent model (COSMO). The SQM/COSMO, Amber/GB and nine widely used SFs have been evaluated in terms ranking power HSP90 protein 72 biologically active compounds 4469 structurally similar decoys. Among conventional SFs, highest early overall enrichment measured by EF 1 AUC% obtained using...
Abstract Invited for this month's cover is the group of Prof. Pavel Hobza, Czech Academy Sciences, Prague. The picture shows a powerful automated quantum mechanics based SQM/COSMO approach to protein–ligand scoring. It comprises thorough preparation ligand structures, extensive generation binding complexes, fast geometry relaxation and reliable affinity prediction. Read full text Minireview at 10.1002/cplu.202000120 .
The stability of the T-shaped and stacked complexes benzene with methanethial (CH2S) methaneselone (CH2Se) their difluoro-, dichloro-, dibromo-derivatives is investigated in ground first electronic excited states by means SCS-ADC2 method. origin stabilization state discussed based on results calculations performed using DFT-SAPT Calculations show that conformers increases upon excitation, while it decreases for most conformers. Both effects are explained changes electrostatic potential (ESP)...
Black‐eyed pea trypsin and chymotrypsin inhibitor (BTCI) is a small protein from Bowman–Birk protease family, which simultaneously inhibits chymotrypsin. Through the inhibition of trypsin‐ chymotrypsin‐like sites on 20S subunit human proteasome, BTCI acts as potent anticarcinogenic agent inducing apoptosis in breast cancer cells. Because lack crystallographic information BTCI‐proteasome complex, we analyze here BTCI‐chymotrypsin BTCI‐trypsin interfaces using computations. We adopt corrected...
The image shows the ability of SQM-based frame to separate actives (background: green spheres) from inactives (red while maintaining a powerful sampling (front: HSP90 crystal complex). Read full text Article at 10.1002/cphc.201900628.
Protein tunnels are essential in transporting small molecules into the active sites of enzymes. Tunnels' geometrical and physico-chemical properties influence transport process. The attractive hot spots for protein engineering drug development. However, studying ligand binding unbinding using experimental techniques is challenging, while silico methods come with their limitations, especially case resource-demanding virtual screening pipelines. Caver Web 1.2 a new version web server combining...