Oriol Gracia Carmona
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Explore the profile of Oriol Gracia Carmona including associated specialties, affiliations and a list of published articles.
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9
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19
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Recent Articles
1.
Carmona O, Kleinjung J, Anastasiou D, Oostenbrink C, Fraternali F
J Mol Biol
. 2025 Feb;
:168969.
PMID: 39900284
Allosteric regulation is crucial for biological processes like signal transduction, transcriptional regulation, and metabolism, yet the mechanisms and macromolecular properties that govern it are still not well understood. Several methods...
2.
Buric F, Viknander S, Fu X, Lemke O, Carmona O, Zrimec J, et al.
Protein Sci
. 2024 Dec;
34(1):e5239.
PMID: 39665261
Understanding what drives protein abundance is essential to biology, medicine, and biotechnology. Driven by evolutionary selection, an amino acid sequence is tailored to meet the required abundance of a proteome,...
3.
Barajas A, Amengual-Rigo P, Pons-Grifols A, Ortiz R, Carmona O, Urrea V, et al.
J Transl Med
. 2024 Jan;
22(1):14.
PMID: 38172991
Background: Neoantigens are patient- and tumor-specific peptides that arise from somatic mutations. They stand as promising targets for personalized therapeutic cancer vaccines. The identification process for neoantigens has evolved with...
4.
Carmona O, Lahham M, Poliak P, Goj D, Friesser E, Wallner S, et al.
J Mol Recognit
. 2023 Nov;
37(2):e3068.
PMID: 37968575
Enzymes are usually stereospecific against chiral substrates, which is commonly accepted for the amine oxidase family of enzymes as well. However, the FsqB (fumisoquin biosynthesis gene B) enzyme that belongs...
5.
Carmona O, Oostenbrink C
J Chem Theory Comput
. 2023 Aug;
19(18):6521-6531.
PMID: 37649349
Molecular dynamics simulations often struggle to obtain sufficient sampling to study complex molecular events due to high energy barriers separating the minima of interest. Multiple enhanced sampling techniques have been...
6.
Carmona O, Gillhofer M, Tomasiak L, De Ruiter A, Oostenbrink C
J Chem Theory Comput
. 2023 May;
19(11):3379-3390.
PMID: 37167545
Determining the presence of water molecules at protein-ligand interfaces is still a challenging task in free-energy calculations. The inappropriate placement of water molecules results in the stabilization of wrong conformational...
7.
Carmona O, Oostenbrink C
J Chem Inf Model
. 2022 Dec;
63(1):197-207.
PMID: 36512416
One of the most challenging aspects in the molecular simulation of proteins is the study of slowly relaxing processes, such as loop rearrangements or ligands that adopt different conformations in...
8.
Mansouri H, Carmona O, Jodlbauer J, Schweiger L, Fink M, Breslmayr E, et al.
ACS Catal
. 2022 Oct;
12(19):11761-11766.
PMID: 36249873
The typically low thermodynamic and kinetic stability of enzymes is a bottleneck for their application in industrial synthesis. Baeyer-Villiger monooxygenases, which oxidize ketones to lactones using aerial oxygen, among other...
9.
Gilabert J, Carmona O, Hogner A, Guallar V
J Chem Inf Model
. 2020 Jul;
60(11):5529-5539.
PMID: 32644807
We present a multistep protocol, combining Monte Carlo and molecular dynamics simulations, for the estimation of absolute binding free energies, one of the most significant challenges in computer-aided drug design....
10.
Gilabert J, Grebner C, Soler D, Lecina D, Municoy M, Carmona O, et al.
J Chem Theory Comput
. 2019 Oct;
15(11):6243-6253.
PMID: 31589430
In this study, we present a fully automatic platform based on our Monte Carlo algorithm, the Protein Energy Landscape Exploration method (PELE), for the estimation of absolute protein-ligand binding free...