Barril X - Search Results

1

Extracting Atomic Contributions to Binding Free Energy Using Molecular Dynamics Simulations with Mixed Solvents (MDmix).

Alvarez-Garcia D, Schmidtke P, Cubero E, Barril X. Alvarez-Garcia D, et al. Among authors: barril x. Curr Drug Discov Technol. 2022;19(2):62-68. doi: 10.2174/1570163819666211223162829. Curr Drug Discov Technol. 2022. PMID: 34951392 Free PMC article.

2

Understanding and predicting druggability. A high-throughput method for detection of drug binding sites.

Schmidtke P, Barril X. Schmidtke P, et al. Among authors: barril x. J Med Chem. 2010 Aug 12;53(15):5858-67. doi: 10.1021/jm100574m. J Med Chem. 2010. PMID: 20684613

3

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories.

Schmidtke P, Bidon-Chanal A, Luque FJ, Barril X. Schmidtke P, et al. Among authors: barril x. Bioinformatics. 2011 Dec 1;27(23):3276-85. doi: 10.1093/bioinformatics/btr550. Epub 2011 Oct 3. Bioinformatics. 2011. PMID: 21967761

4

Shielded hydrogen bonds as structural determinants of binding kinetics: application in drug design.

Schmidtke P, Luque FJ, Murray JB, Barril X. Schmidtke P, et al. Among authors: barril x. J Am Chem Soc. 2011 Nov 23;133(46):18903-10. doi: 10.1021/ja207494u. Epub 2011 Oct 28. J Am Chem Soc. 2011. PMID: 21981450

5

rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids.

Ruiz-Carmona S, Alvarez-Garcia D, Foloppe N, Garmendia-Doval AB, Juhos S, Schmidtke P, Barril X, Hubbard RE, Morley SD. Ruiz-Carmona S, et al. Among authors: barril x. PLoS Comput Biol. 2014 Apr 10;10(4):e1003571. doi: 10.1371/journal.pcbi.1003571. eCollection 2014 Apr. PLoS Comput Biol. 2014. PMID: 24722481 Free PMC article.

6

Molecular simulations with solvent competition quantify water displaceability and provide accurate interaction maps of protein binding sites.

Alvarez-Garcia D, Barril X. Alvarez-Garcia D, et al. Among authors: barril x. J Med Chem. 2014 Oct 23;57(20):8530-9. doi: 10.1021/jm5010418. Epub 2014 Oct 14. J Med Chem. 2014. PMID: 25275946

7

In Silico/In Vivo Insights into the Functional and Evolutionary Pathway of Pseudomonas aeruginosa Oleate-Diol Synthase. Discovery of a New Bacterial Di-Heme Cytochrome C Peroxidase Subfamily.

Estupiñán M, Álvarez-García D, Barril X, Diaz P, Manresa A. Estupiñán M, et al. Among authors: barril x. PLoS One. 2015 Jul 8;10(7):e0131462. doi: 10.1371/journal.pone.0131462. eCollection 2015. PLoS One. 2015. PMID: 26154497 Free PMC article.

8

Relationship between Protein Flexibility and Binding: Lessons for Structure-Based Drug Design.

Alvarez-Garcia D, Barril X. Alvarez-Garcia D, et al. Among authors: barril x. J Chem Theory Comput. 2014 Jun 10;10(6):2608-14. doi: 10.1021/ct500182z. Epub 2014 May 30. J Chem Theory Comput. 2014. PMID: 26580781

9

Binding kinetics in drug discovery.

Barril X, Danielsson H. Barril X, et al. Drug Discov Today Technol. 2015 Oct;17:35-6. doi: 10.1016/j.ddtec.2015.10.011. Epub 2015 Dec 10. Drug Discov Today Technol. 2015. PMID: 26724335 No abstract available.

10

Dynamic undocking and the quasi-bound state as tools for drug discovery.

Ruiz-Carmona S, Schmidtke P, Luque FJ, Baker L, Matassova N, Davis B, Roughley S, Murray J, Hubbard R, Barril X. Ruiz-Carmona S, et al. Among authors: barril x. Nat Chem. 2017 Mar;9(3):201-206. doi: 10.1038/nchem.2660. Epub 2016 Nov 14. Nat Chem. 2017. PMID: 28221352

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