Adam Pecina
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Explore the profile of Adam Pecina including associated specialties, affiliations and a list of published articles.
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20
Citations
124
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Recent Articles
1.
Kramer C, Chodera J, Damm-Ganamet K, Gilson M, Gunther J, Lessel U, et al.
J Chem Inf Model
. 2025 Feb;
65(5):2180-2190.
PMID: 39951479
Computational tools for structure-based drug design (SBDD) are widely used in drug discovery and can provide valuable insights to advance projects in an efficient and cost-effective manner. However, despite the...
2.
Bach K, Dohnalek J, Skerlova J, Kuzmik J, Polachova E, Stanchev S, et al.
Eur J Med Chem
. 2024 Jun;
275:116606.
PMID: 38901105
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,...
3.
Pecina A, Fanfrlik J, Lepsik M, rezac J
Nat Commun
. 2024 Feb;
15(1):1127.
PMID: 38321025
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...
4.
Pecina A, Rosa-Gastaldo D, Riccardi L, Franco-Ulloa S, Milan E, Scrimin P, et al.
ACS Catal
. 2021 Sep;
11(14):8736-8748.
PMID: 34476110
Recent studies have shown that gold nanoparticles (AuNPs) functionalized with Zn(II) complexes can cleave phosphate esters and nucleic acids. Remarkably, such synthetic nanonucleases appear to catalyze metal (Zn)-aided hydrolytic reactions...
5.
Fanfrlik J, Pecina A, rezac J, Lepsik M, Sarosi M, Hnyk D, et al.
Chemphyschem
. 2020 Nov;
21(23):2599-2604.
PMID: 33179424
The success of approximate computational methods, such as molecular mechanics, or dispersion-corrected density functional theory, in the description of non-covalent interactions relies on accurate parameterizations. Benchmark data sets are thus...
6.
Pecina A, Eyrilmez S, Kopruluoglu C, Miriyala V, Lepsik M, Fanfrlik J, et al.
Chempluschem
. 2020 Sep;
85(11):2361.
PMID: 32986310
Invited for this month's cover is the group of Prof. Pavel Hobza, Czech Academy of Sciences, Prague. The cover picture shows a powerful automated quantum mechanics based SQM/COSMO approach to...
7.
Czescik J, Zamolo S, Darbre T, Rigo R, Sissi C, Pecina A, et al.
Angew Chem Int Ed Engl
. 2020 Sep;
60(3):1423-1432.
PMID: 32985766
Similarly to enzymes, functionalized gold nanoparticles efficiently catalyze chemical reactions, hence the term nanozymes. Herein, we present our results showing how surface-passivated gold nanoparticles behave as synthetic nanonucleases, able to...
8.
Pecina A, Eyrilmez S, Kopruluoglu C, Miriyala V, Lepsik M, Fanfrlik J, et al.
Chempluschem
. 2020 Jul;
85(11):2362-2371.
PMID: 32609421
Quantum mechanical (QM) methods have been gaining importance in structure-based drug design where a reliable description of protein-ligand interactions is of utmost significance. However, strategies i. e. QM/MM, fragmentation or...
9.
Lepsik M, rezac J, Kolar M, Pecina A, Hobza P, Fanfrlik J
Chempluschem
. 2020 Jan;
78(9):921-931.
PMID: 31986741
This Minireview discusses the latest developments in modern quantum mechanics (QM)-based computer-aided drug design, especially using semiempirical QM (SQM) methods. It first tackles biochemical and biophysical quantities and the approaches...
10.
Ajani H, Pecina A, Eyrilmez S, Fanfrlik J, Haldar S, rezac J, et al.
ACS Omega
. 2018 Jul;
2(7):4022-4029.
PMID: 30023710
General and reliable description of structures and energetics in protein-ligand (PL) binding using the docking/scoring methodology has until now been elusive. We address this urgent deficiency of scoring functions (SFs)...