Search results
- 1.0582928 - ÚOCHB 2025 RIV US eng J - Journal Article
Pecina, Adam - Fanfrlík, Jindřich - Lepšík, Martin - Řezáč, Jan
SQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein-ligand binding affinity predictions in minutes.
Nature Communications. Roč. 15, February (2024), č. článku 1127. E-ISSN 2041-1723
Research Infrastructure: e-INFRA CZ II - 90254
Institutional support: RVO:61388963
Keywords : NDDO approximations * free-energies * docking
Impact factor: 16.6, year: 2022
Method of publishing: Open access
https://doi.org/10.1038/s41467-024-45431-8
Permanent Link: https://hdl.handle.net/11104/0350971
Research data: ZENODO - 2.0535455 - ÚOCHB 2021 RIV DE eng J - Journal Article
Fanfrlík, Jindřich - Pecina, Adam - Řezáč, Jan - Lepšík, Martin - Sárosi, M. B. - Hnyk, Drahomír - Hobza, Pavel
Benchmark Data Sets of Boron Cluster Dihydrogen Bonding for the Validation of Approximate Computational Methods.
ChemPhysChem. Roč. 21, č. 23 (2020), s. 2599-2604. ISSN 1439-4235. E-ISSN 1439-7641
R&D Projects: GA MŠMT(CZ) EF16_019/0000729; GA ČR(CZ) GA19-17156S; GA ČR(CZ) GA19-13905S
Institutional support: RVO:61388963 ; RVO:61388980
Keywords : carbaborane * CCSD(T) * DFT-D3 * molecular mechanics * noncovalent interactions
OECD category: Physical chemistry; Inorganic and nuclear chemistry (UACH-T)
Impact factor: 3.102, year: 2020
Method of publishing: Limited access
https://doi.org/10.1002/cphc.202000729
Permanent Link: http://hdl.handle.net/11104/0313518 - 3.0531546 - ÚOCHB 2021 RIV DE eng J - Journal Article
Pecina, Adam - Eyrilmez, Saltuk M. - Köprülüoglu, Cemal - Miriyala, Vijay Madhav - Lepšík, Martin - Fanfrlík, Jindřich - Řezáč, Jan - Hobza, Pavel
SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design.
ChemPlusChem. Roč. 85, č. 11 (2020), s. 2362-2371. ISSN 2192-6506. E-ISSN 2192-6506
R&D Projects: GA MŠMT(CZ) EF16_019/0000729
Institutional support: RVO:61388963
Keywords : in silico drug design * protein-ligand binding * quantum mechanics * semiempirical methods * virtual screening
OECD category: Physical chemistry
Impact factor: 2.863, year: 2020
Method of publishing: Limited access
https://doi.org/10.1002/cplu.202000120
Permanent Link: http://hdl.handle.net/11104/0310179 - 4.0495770 - ÚOCHB 2019 RIV DE eng J - Journal Article
Honda, D. E. - Martins, J. B. L. - Ventura, M. M. - Eyrilmez, Saltuk M. - Lepšík, Martin - Hobza, Pavel - Pecina, Adam - de Freitas, S. M.
Interface Interactions of the Bowman-Birk Inhibitor BTCI in a Ternary Complex with Trypsin and Chymotrypsin Evaluated by Semiempirical Quantum Mechanical Calculations.
European Journal of Organic Chemistry. Roč. 2018, č. 37 (2018), s. 5203-5211. ISSN 1434-193X. E-ISSN 1099-0690
R&D Projects: GA MŠMT(CZ) EF16_019/0000729
Institutional support: RVO:61388963
Keywords : protein-protein interactions * protease inhibitors * protein structures * interaction energy * amino acids * interfaces
OECD category: Physical chemistry
Impact factor: 3.029, year: 2018
Permanent Link: http://hdl.handle.net/11104/0288692 - 5.0490170 - ÚOCHB 2019 RIV DE eng J - Journal Article
Pecina, Adam - Brynda, Jiří - Vrzal, Lukáš - Gnanasekaran, Ramachandran - Hořejší, M. - Eyrilmez, Saltuk M. - Řezáč, Jan - Lepšík, Martin - Řezáčová, Pavlína - Hobza, Pavel - Majer, Pavel - Veverka, Václav - Fanfrlík, Jindřich
Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes.
ChemPhysChem. Roč. 19, č. 7 (2018), s. 873-879. ISSN 1439-4235. E-ISSN 1439-7641
R&D Projects: GA ČR(CZ) GJ16-11321Y; GA MŠMT(CZ) LO1304; GA MŠMT(CZ) LK11205; GA MŠMT(CZ) EF16_019/0000729
Institutional support: RVO:61388963
Keywords : binding affinities * crystallography * lead optimization * quantum mechanics * scoring function
OECD category: Physical chemistry
Impact factor: 3.077, year: 2018
Permanent Link: http://hdl.handle.net/11104/0284458 - 6.0487122 - ÚOCHB 2018 RIV US eng J - Journal Article
Ajani, Haresh - Pecina, Adam - Eyrilmez, Saltuk M. - Fanfrlík, Jindřich - Haldar, Susanta - Řezáč, Jan - Hobza, Pavel - Lepšík, Martin
Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein-Ligand Complexes in Cognate Docking.
ACS Omega. Roč. 2, č. 7 (2017), s. 4022-4029. ISSN 2470-1343. E-ISSN 2470-1343
R&D Projects: GA ČR(CZ) GBP208/12/G016; GA ČR(CZ) GJ16-11321Y
Institutional support: RVO:61388963
Keywords : aldose reductase inhibition * biological applications * mechanical calculations
OECD category: Physical chemistry
https://pubs.acs.org/doi/full/10.1021/acsomega.7b00503
Permanent Link: http://hdl.handle.net/11104/0281802 - 7.0477552 - ÚOCHB 2018 RIV GB eng J - Journal Article
Fanfrlík, Jindřich - Pecina, Adam - Řezáč, Jan - Sedlák, Robert - Hnyk, Drahomír - Lepšík, Martin - Hobza, Pavel
B-H center dot center dot center dot pi: a nonclassical hydrogen bond or dispersion contact?
Physical Chemistry Chemical Physics. Roč. 19, č. 28 (2017), s. 18194-18200. ISSN 1463-9076. E-ISSN 1463-9084
R&D Projects: GA ČR(CZ) GBP208/12/G016; GA ČR(CZ) GA17-08045S
Institutional support: RVO:61388963 ; RVO:61388980
Keywords : perturbation theory * intermolecular interactions * interaction energies
OECD category: Physical chemistry; Inorganic and nuclear chemistry (UACH-T)
Impact factor: 3.906, year: 2017
http://pubs.rsc.org/en/content/articlehtml/2017/cp/c7cp02762a
Permanent Link: http://hdl.handle.net/11104/0273871 - 8.0475086 - ÚOCHB 2018 RIV US eng J - Journal Article
Pecina, Adam - Haldar, Susanta - Fanfrlík, Jindřich - Meier, R. - Řezáč, Jan - Lepšík, Martin - Hobza, Pavel
SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses.
Journal of Chemical Information and Modeling. Roč. 57, č. 2 (2017), s. 127-132. ISSN 1549-9596. E-ISSN 1549-960X
R&D Projects: GA ČR(CZ) GBP208/12/G016; GA ČR(CZ) GJ16-11321Y
Institutional support: RVO:61388963
Keywords : aldose reductase inhibition * binding affinity * PM6 method
OECD category: Physical chemistry
Impact factor: 3.804, year: 2017
Permanent Link: http://hdl.handle.net/11104/0271962 - 9.0458893 - ÚOCHB 2017 RIV GB eng J - Journal Article
Pecina, Adam - Meier, R. - Fanfrlík, Jindřich - Lepšík, Martin - Řezáč, Jan - Hobza, Pavel - Baldauf, C.
The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein-ligand interactions and implicit COSMO solvation.
Chemical Communications. Roč. 52, č. 16 (2016), s. 3312-3315. ISSN 1359-7345. E-ISSN 1364-548X
R&D Projects: GA ČR GBP208/12/G016
Institutional support: RVO:61388963
Keywords : empirical scoring functions * density functional theory * binding affinity
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 6.319, year: 2016
http://pubs.rsc.org/en/content/articlepdf/2016/cc/c5cc09499b
Permanent Link: http://hdl.handle.net/11104/0259109File Download Size Commentary Version Access 0458893.pdf 1 2 MB Publisher’s postprint open-access - 10.0458449 - ÚOCHB 2017 RIV GB eng J - Journal Article
Fanfrlík, Jindřich - Sedlák, Robert - Pecina, Adam - Rulíšek, Lubomír - Dostál, L. - Moncól, J. - Růžička, A. - Hobza, Pavel
The non-planarity of the benzene molecule in the X-ray structure of the chelated bismuth(III) heteroboroxine complex is not supported by quantum mechanical calculations.
Dalton Transactions. Roč. 45, č. 2 (2016), s. 462-465. ISSN 1477-9226. E-ISSN 1477-9234
R&D Projects: GA ČR GBP208/12/G016; GA ČR(CZ) GA14-31419S
Institutional support: RVO:61388963
Keywords : crystal structures * arene complexes * sigma hole
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 4.029, year: 2016
http://pubs.rsc.org/en/content/articlepdf/2016/dt/c5dt04381f
Permanent Link: http://hdl.handle.net/11104/0258729