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Items: 1 to 50 of 69

1.

Cosolvent-Based Protein Pharmacophore for Ligand Enrichment in Virtual Screening.

Arcon JP, Defelipe LA, Lopez ED, Burastero O, Modenutti CP, Barril X, Marti MA, Turjanski AG.

J Chem Inf Model. 2019 Aug 26;59(8):3572-3583. doi: 10.1021/acs.jcim.9b00371. Epub 2019 Aug 16.

PMID:
31373819
2.

DUckCov: a Dynamic Undocking-Based Virtual Screening Protocol for Covalent Binders.

Rachman M, Scarpino A, Bajusz D, Pálfy G, Vida I, Perczel A, Barril X, Keserű GM.

ChemMedChem. 2019 May 17;14(10):1011-1021. doi: 10.1002/cmdc.201900078. Epub 2019 Mar 8.

3.

Solvents to Fragments to Drugs: MD Applications in Drug Design.

Defelipe LA, Arcon JP, Modenutti CP, Marti MA, Turjanski AG, Barril X.

Molecules. 2018 Dec 11;23(12). pii: E3269. doi: 10.3390/molecules23123269. Review.

4.

Predicting how drug molecules bind to their protein targets.

Rachman MM, Barril X, Hubbard RE.

Curr Opin Pharmacol. 2018 Oct;42:34-39. doi: 10.1016/j.coph.2018.07.001. Epub 2018 Jul 21. Review.

PMID:
30041063
5.

Dynamic Undocking: A Novel Method for Structure-Based Drug Discovery.

Majewski M, Ruiz-Carmona S, Barril X.

Methods Mol Biol. 2018;1824:195-215. doi: 10.1007/978-1-4939-8630-9_11.

PMID:
30039408
6.

Correction to Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking and Allows Accurate Binding Free Energy Predictions.

Arcon JP, Defelipe LA, Modenutti CP, López ED, Alvarez Garcia D, Barril X, Turjanski AG, Martí MA.

J Chem Inf Model. 2018 Jun 25;58(6):1312. doi: 10.1021/acs.jcim.8b00299. Epub 2018 Jun 13. No abstract available.

PMID:
29897744
7.

Computer-aided drug design: time to play with novel chemical matter.

Barril X.

Expert Opin Drug Discov. 2017 Oct;12(10):977-980. doi: 10.1080/17460441.2017.1362386. Epub 2017 Aug 3. No abstract available.

PMID:
28756685
8.

Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR.

Westermaier Y, Ruiz-Carmona S, Theret I, Perron-Sierra F, Poissonnet G, Dacquet C, Boutin JA, Ducrot P, Barril X.

J Comput Aided Mol Des. 2017 Aug;31(8):755-775. doi: 10.1007/s10822-017-0040-7. Epub 2017 Jul 15.

PMID:
28712038
9.

LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening.

Radusky L, Ruiz-Carmona S, Modenutti C, Barril X, Turjanski AG, Martí MA.

J Chem Inf Model. 2017 Aug 28;57(8):1741-1746. doi: 10.1021/acs.jcim.7b00241. Epub 2017 Jul 27.

PMID:
28700230
10.

Detecting similar binding pockets to enable systems polypharmacology.

Duran-Frigola M, Siragusa L, Ruppin E, Barril X, Cruciani G, Aloy P.

PLoS Comput Biol. 2017 Jun 29;13(6):e1005522. doi: 10.1371/journal.pcbi.1005522. eCollection 2017 Jun.

11.

Identification and Characterization of a Secondary Sodium-Binding Site and the Main Selectivity Determinants in the Human Concentrative Nucleoside Transporter 3.

Arimany-Nardi C, Claudio-Montero A, Viel-Oliva A, Schmidtke P, Estarellas C, Barril X, Bidon-Chanal A, Pastor-Anglada M.

Mol Pharm. 2017 Jun 5;14(6):1980-1987. doi: 10.1021/acs.molpharmaceut.7b00085. Epub 2017 May 9.

PMID:
28441873
12.

Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions.

Arcon JP, Defelipe LA, Modenutti CP, López ED, Alvarez-Garcia D, Barril X, Turjanski AG, Martí MA.

J Chem Inf Model. 2017 Apr 24;57(4):846-863. doi: 10.1021/acs.jcim.6b00678. Epub 2017 Mar 31. Erratum in: J Chem Inf Model. 2018 Jun 25;58(6):1312.

PMID:
28318252
13.

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.

Nat Chem. 2017 Mar;9(3):201-206. doi: 10.1038/nchem.2660. Epub 2016 Nov 14.

PMID:
28221352
14.

Docking-undocking combination applied to the D3R Grand Challenge 2015.

Ruiz-Carmona S, Barril X.

J Comput Aided Mol Des. 2016 Sep;30(9):805-815. Epub 2016 Oct 5.

PMID:
27709317
15.

Inherent conformational flexibility of F1-ATPase α-subunit.

Hahn-Herrera O, Salcedo G, Barril X, García-Hernández E.

Biochim Biophys Acta. 2016 Sep;1857(9):1392-1402. doi: 10.1016/j.bbabio.2016.04.283. Epub 2016 Apr 29.

16.

Binding kinetics in drug discovery.

Barril X, Danielsson H.

Drug Discov Today Technol. 2015 Oct;17:35-6. doi: 10.1016/j.ddtec.2015.10.011. Epub 2015 Dec 10. No abstract available.

PMID:
26724335
17.

Combined Use of Oligopeptides, Fragment Libraries, and Natural Compounds: A Comprehensive Approach To Sample the Druggability of Vascular Endothelial Growth Factor.

Bayó-Puxan N, Rodríguez-Mias R, Goldflam M, Kotev M, Ciudad S, Hipolito CJ, Varese M, Suga H, Campos-Olivas R, Barril X, Guallar V, Teixidó M, García J, Giralt E.

ChemMedChem. 2016 Apr 19;11(8):928-39. doi: 10.1002/cmdc.201500467. Epub 2015 Nov 10.

18.

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.

PLoS One. 2015 Jul 8;10(7):e0131462. doi: 10.1371/journal.pone.0131462. eCollection 2015.

19.

Assessing the suitability of the multilevel strategy for the conformational analysis of small ligands.

Juárez-Jiménez J, Barril X, Orozco M, Pouplana R, Luque FJ.

J Phys Chem B. 2015 Jan 22;119(3):1164-72. doi: 10.1021/jp506779y. Epub 2014 Oct 29.

PMID:
25319869
20.

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

Alvarez-Garcia D, Barril X.

J Med Chem. 2014 Oct 23;57(20):8530-9. doi: 10.1021/jm5010418. Epub 2014 Oct 14.

PMID:
25275946
21.

Virtual screening: an in silico tool for interlacing the chemical universe with the proteome.

Westermaier Y, Barril X, Scapozza L.

Methods. 2015 Jan;71:44-57. doi: 10.1016/j.ymeth.2014.08.001. Epub 2014 Sep 2.

PMID:
25193260
22.

Ligand discovery: Docking points.

Barril X.

Nat Chem. 2014 Jul;6(7):560-1. doi: 10.1038/nchem.1986. No abstract available.

PMID:
24950321
23.

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

Alvarez-Garcia D, Barril X.

J Chem Theory Comput. 2014 Jun 10;10(6):2608-14. doi: 10.1021/ct500182z. Epub 2014 May 30.

PMID:
26580781
24.

VAV3 mediates resistance to breast cancer endocrine therapy.

Aguilar H, Urruticoechea A, Halonen P, Kiyotani K, Mushiroda T, Barril X, Serra-Musach J, Islam A, Caizzi L, Di Croce L, Nevedomskaya E, Zwart W, Bostner J, Karlsson E, Pérez Tenorio G, Fornander T, Sgroi DC, Garcia-Mata R, Jansen MP, García N, Bonifaci N, Climent F, Soler MT, Rodríguez-Vida A, Gil M, Brunet J, Martrat G, Gómez-Baldó L, Extremera AI, Figueras A, Balart J, Clarke R, Burnstein KL, Carlson KE, Katzenellenbogen JA, Vizoso M, Esteller M, Villanueva A, Rodríguez-Peña AB, Bustelo XR, Nakamura Y, Zembutsu H, Stål O, Beijersbergen RL, Pujana MA.

Breast Cancer Res. 2014 May 28;16(3):R53. doi: 10.1186/bcr3664.

25.

TuberQ: a Mycobacterium tuberculosis protein druggability database.

Radusky L, Defelipe LA, Lanzarotti E, Luque J, Barril X, Marti MA, Turjanski AG.

Database (Oxford). 2014 May 8;2014(0):bau035. doi: 10.1093/database/bau035. Print 2014.

26.

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.

PLoS Comput Biol. 2014 Apr 10;10(4):e1003571. doi: 10.1371/journal.pcbi.1003571. eCollection 2014 Apr.

27.

Pharmacological chaperones for enzyme enhancement therapy in genetic diseases.

Aymami J, Barril X, Rodríguez-Pascau L, Martinell M.

Pharm Pat Anal. 2013 Jan;2(1):109-24. doi: 10.4155/ppa.12.74. Review.

PMID:
24236974
28.

A Multilevel Strategy for the Exploration of the Conformational Flexibility of Small Molecules.

Forti F, Cavasotto CN, Orozco M, Barril X, Luque FJ.

J Chem Theory Comput. 2012 May 8;8(5):1808-19. doi: 10.1021/ct300097s. Epub 2012 Apr 10.

PMID:
26593672
29.

Molecular simulation methods in drug discovery: a prospective outlook.

Barril X, Luque FJ.

J Comput Aided Mol Des. 2012 Jan;26(1):81-6. doi: 10.1007/s10822-011-9506-1. Epub 2011 Dec 8.

PMID:
22160626
30.

Allosteric regulation of PKCθ: understanding multistep phosphorylation and priming by ligands in AGC kinases.

Seco J, Ferrer-Costa C, Campanera JM, Soliva R, Barril X.

Proteins. 2012 Jan;80(1):269-80. doi: 10.1002/prot.23205. Epub 2011 Nov 9.

PMID:
22072623
31.

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

Schmidtke P, Luque FJ, Murray JB, Barril X.

J Am Chem Soc. 2011 Nov 23;133(46):18903-10. doi: 10.1021/ja207494u. Epub 2011 Oct 28.

PMID:
21981450
32.

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

Schmidtke P, Bidon-Chanal A, Luque FJ, Barril X.

Bioinformatics. 2011 Dec 1;27(23):3276-85. doi: 10.1093/bioinformatics/btr550. Epub 2011 Oct 3.

PMID:
21967761
33.

Protein flexibility and ligand recognition: challenges for molecular modeling.

Spyrakis F, BidonChanal A, Barril X, Luque FJ.

Curr Top Med Chem. 2011;11(2):192-210. Review.

PMID:
20939788
34.

Ensemble Docking from Homology Models.

Novoa EM, Ribas de Pouplana L, Barril X, Orozco M.

J Chem Theory Comput. 2010 Aug 10;6(8):2547-57. doi: 10.1021/ct100246y. Epub 2010 Jul 16.

PMID:
26613506
35.

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

Schmidtke P, Barril X.

J Med Chem. 2010 Aug 12;53(15):5858-67. doi: 10.1021/jm100574m.

PMID:
20684613
36.

Combining hit identification strategies: fragment-based and in silico approaches to orally active 2-aminothieno[2,3-d]pyrimidine inhibitors of the Hsp90 molecular chaperone.

Brough PA, Barril X, Borgognoni J, Chene P, Davies NG, Davis B, Drysdale MJ, Dymock B, Eccles SA, Garcia-Echeverria C, Fromont C, Hayes A, Hubbard RE, Jordan AM, Jensen MR, Massey A, Merrett A, Padfield A, Parsons R, Radimerski T, Raynaud FI, Robertson A, Roughley SD, Schoepfer J, Simmonite H, Sharp SY, Surgenor A, Valenti M, Walls S, Webb P, Wood M, Workman P, Wright L.

J Med Chem. 2009 Aug 13;52(15):4794-809. doi: 10.1021/jm900357y.

PMID:
19610616
37.

Tacripyrines, the first tacrine-dihydropyridine hybrids, as multitarget-directed ligands for the treatment of Alzheimer's disease.

Marco-Contelles J, León R, de los Ríos C, Samadi A, Bartolini M, Andrisano V, Huertas O, Barril X, Luque FJ, Rodríguez-Franco MI, López B, López MG, García AG, Carreiras Mdo C, Villarroya M.

J Med Chem. 2009 May 14;52(9):2724-32. doi: 10.1021/jm801292b.

PMID:
19374444
38.

Binding site detection and druggability index from first principles.

Seco J, Luque FJ, Barril X.

J Med Chem. 2009 Apr 23;52(8):2363-71. doi: 10.1021/jm801385d.

PMID:
19296650
39.

Toward accurate relative energy predictions of the bioactive conformation of drugs.

Butler KT, Luque FJ, Barril X.

J Comput Chem. 2009 Mar;30(4):601-10. doi: 10.1002/jcc.21087.

PMID:
18711721
40.

New tacrine-dihydropyridine hybrids that inhibit acetylcholinesterase, calcium entry, and exhibit neuroprotection properties.

León R, de los Ríos C, Marco-Contelles J, Huertas O, Barril X, Luque FJ, López MG, García AG, Villarroya M.

Bioorg Med Chem. 2008 Aug 15;16(16):7759-69. doi: 10.1016/j.bmc.2008.07.005. Epub 2008 Jul 8.

PMID:
18640842
41.

NVP-AUY922: a novel heat shock protein 90 inhibitor active against xenograft tumor growth, angiogenesis, and metastasis.

Eccles SA, Massey A, Raynaud FI, Sharp SY, Box G, Valenti M, Patterson L, de Haven Brandon A, Gowan S, Boxall F, Aherne W, Rowlands M, Hayes A, Martins V, Urban F, Boxall K, Prodromou C, Pearl L, James K, Matthews TP, Cheung KM, Kalusa A, Jones K, McDonald E, Barril X, Brough PA, Cansfield JE, Dymock B, Drysdale MJ, Finch H, Howes R, Hubbard RE, Surgenor A, Webb P, Wood M, Wright L, Workman P.

Cancer Res. 2008 Apr 15;68(8):2850-60. doi: 10.1158/0008-5472.CAN-07-5256.

42.

4,5-diarylisoxazole Hsp90 chaperone inhibitors: potential therapeutic agents for the treatment of cancer.

Brough PA, Aherne W, Barril X, Borgognoni J, Boxall K, Cansfield JE, Cheung KM, Collins I, Davies NG, Drysdale MJ, Dymock B, Eccles SA, Finch H, Fink A, Hayes A, Howes R, Hubbard RE, James K, Jordan AM, Lockie A, Martins V, Massey A, Matthews TP, McDonald E, Northfield CJ, Pearl LH, Prodromou C, Ray S, Raynaud FI, Roughley SD, Sharp SY, Surgenor A, Walmsley DL, Webb P, Wood M, Workman P, Wright L.

J Med Chem. 2008 Jan 24;51(2):196-218. Epub 2007 Nov 20.

PMID:
18020435
43.

Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian.

Forti F, Barril X, Luque FJ, Orozco M.

J Comput Chem. 2008 Mar;29(4):578-87.

PMID:
17705247
44.

Inhibition of the heat shock protein 90 molecular chaperone in vitro and in vivo by novel, synthetic, potent resorcinylic pyrazole/isoxazole amide analogues.

Sharp SY, Prodromou C, Boxall K, Powers MV, Holmes JL, Box G, Matthews TP, Cheung KM, Kalusa A, James K, Hayes A, Hardcastle A, Dymock B, Brough PA, Barril X, Cansfield JE, Wright L, Surgenor A, Foloppe N, Hubbard RE, Aherne W, Pearl L, Jones K, McDonald E, Raynaud F, Eccles S, Drysdale M, Workman P.

Mol Cancer Ther. 2007 Apr;6(4):1198-211.

45.

Molecular modelling.

Barril X, Soliva R.

Mol Biosyst. 2006 Dec;2(12):660-81. Epub 2006 Oct 19. No abstract available.

PMID:
17216047
46.

A hydrophobic similarity analysis of solvation effects on nucleic acid bases.

Muñoz-Muriedas J, Barril X, López JM, Orozco M, Luque FJ.

J Mol Model. 2007 Feb;13(2):357-65. Epub 2006 Sep 21.

PMID:
17024407
47.

Incorporating protein flexibility into docking and structure-based drug design.

Barril X, Fradera X.

Expert Opin Drug Discov. 2006 Sep;1(4):335-49. doi: 10.1517/17460441.1.4.335.

PMID:
23495904
48.

4-Amino derivatives of the Hsp90 inhibitor CCT018159.

Barril X, Beswick MC, Collier A, Drysdale MJ, Dymock BW, Fink A, Grant K, Howes R, Jordan AM, Massey A, Surgenor A, Wayne J, Workman P, Wright L.

Bioorg Med Chem Lett. 2006 May 1;16(9):2543-8. Epub 2006 Feb 9.

PMID:
16480864
49.

A fluorescence polarization assay for inhibitors of Hsp90.

Howes R, Barril X, Dymock BW, Grant K, Northfield CJ, Robertson AG, Surgenor A, Wayne J, Wright L, James K, Matthews T, Cheung KM, McDonald E, Workman P, Drysdale MJ.

Anal Biochem. 2006 Mar 15;350(2):202-13. Epub 2006 Jan 23.

PMID:
16460658
50.

3-(5-Chloro-2,4-dihydroxyphenyl)-pyrazole-4-carboxamides as inhibitors of the Hsp90 molecular chaperone.

Brough PA, Barril X, Beswick M, Dymock BW, Drysdale MJ, Wright L, Grant K, Massey A, Surgenor A, Workman P.

Bioorg Med Chem Lett. 2005 Dec 1;15(23):5197-201. Epub 2005 Oct 5.

PMID:
16213716

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