Works matching AU Barril, Xavier

Results: 35

Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase.

Published in:

ChemBioChem, 2021, v. 22, n. 9, p. 1597, doi. 10.1002/cbic.202000736

By:

Talibov, Vladimir O.;
Fabini, Edoardo;
FitzGerald, Edward A.;
Tedesco, Daniele;
Cederfeldt, Daniela;
Talu, Martin J.;
Rachman, Moira M.;
Mihalic, Filip;
Manoni, Elisabetta;
Naldi, Marina;
Sanese, Paola;
Forte, Giovanna;
Lepore Signorile, Martina;
Barril, Xavier;
Simone, Cristiano;
Bartolini, Manuela;
Dobritzsch, Doreen;
Del Rio, Alberto;
Danielson, U. Helena

Publication type:

Article

Comprehensive detection and characterization of human druggable pockets through binding site descriptors.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52146-3

By:

Comajuncosa-Creus, Arnau;
Jorba, Guillem;
Barril, Xavier;
Aloy, Patrick

Publication type:

Article

Improvements in docking scoring functions: the physics-based perspective.

Published in:

2012

By:

Barril, Xavier

Publication type:

Abstract

Ligand discovery: Docking points.

Published in:

Nature Chemistry, 2014, v. 6, n. 7, p. 560, doi. 10.1038/nchem.1986

By:

Barril, Xavier

Publication type:

Article

Extended connectivity interaction features: improving binding affinity prediction through chemical description.

Published in:

Bioinformatics, 2021, v. 37, n. 10, p. 1376, doi. 10.1093/bioinformatics/btaa982

By:

Sánchez-Cruz, Norberto;
Medina-Franco, José L;
Mestres, Jordi;
Barril, Xavier

Publication type:

Article

Druggability predictions: methods, limitations, and applications.

Published in:

WIREs: Computational Molecular Science, 2013, v. 3, n. 4, p. 327, doi. 10.1002/wcms.1134

By:

Barril, Xavier

Publication type:

Article

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

Published in:

Journal of Molecular Modeling, 2007, v. 13, n. 2, p. 357

By:

Jordi Muñoz-Muriedas;
Xavier Barril;
José López;
Francisco Luque

Publication type:

Article

Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins.

Published in:

Proteins, 2001, v. 45, n. 4, p. 428, doi. 10.1002/prot.1159

By:

Gelpí, Josep Lluis;
Kalko, Susana G.;
Barril, Xavier;
Cirera, Jordi;
de la Cruz, Xavier;
Luque, F. Javier;
Orozco, Modesto

Publication type:

Article

Detecting similar binding pockets to enable systems polypharmacology.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 6, p. 1, doi. 10.1371/journal.pcbi.1005522

By:

Duran-Frigola, Miquel;
Siragusa, Lydia;
Ruppin, Eytan;
Barril, Xavier;
Cruciani, Gabriele;
Aloy, Patrick

Publication type:

Article

Computational Design of Inhibitors Targeting the Catalytic β Subunit of Escherichia coli F O F 1 -ATP Synthase.

Published in:

Antibiotics (2079-6382), 2022, v. 11, n. 5, p. 557, doi. 10.3390/antibiotics11050557

By:

Avila-Barrientos, Luis Pablo;
Cofas-Vargas, Luis Fernando;
Agüero-Chapin, Guillermin;
Hernández-García, Enrique;
Ruiz-Carmona, Sergio;
Valdez-Cruz, Norma A.;
Trujillo-Roldán, Mauricio;
Weber, Joachim;
Ruiz-Blanco, Yasser B.;
Barril, Xavier;
García-Hernández, Enrique

Publication type:

Article

Development of an Automatic Pipeline for Participation in the CELPP Challenge.

Published in:

International Journal of Molecular Sciences, 2022, v. 23, n. 9, p. 4756, doi. 10.3390/ijms23094756

By:

Miñarro-Lleonar, Marina;
Ruiz-Carmona, Sergio;
Alvarez-Garcia, Daniel;
Schmidtke, Peter;
Barril, Xavier

Publication type:

Article

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

Published in:

Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 8, p. 755, doi. 10.1007/s10822-017-0040-7

By:

Westermaier, Yvonne;
Ruiz-Carmona, Sergio;
Theret, Isabelle;
Perron-Sierra, Françoise;
Poissonnet, Guillaume;
Dacquet, Catherine;
Boutin, Jean;
Ducrot, Pierre;
Barril, Xavier

Publication type:

Article

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

Published in:

Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 9, p. 805, doi. 10.1007/s10822-016-9979-z

By:

Ruiz-Carmona, Sergio;
Barril, Xavier

Publication type:

Article

Molecular simulation methods in drug discovery: a prospective outlook.

Published in:

Journal of Computer-Aided Molecular Design, 2012, v. 26, n. 1, p. 81, doi. 10.1007/s10822-011-9506-1

By:

Barril, Xavier;
Javier Luque, F.

Publication type:

Article

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

Published in:

Bioinformatics, 2011, v. 27, n. 23, p. 3276, doi. 10.1093/bioinformatics/btr550

By:

Schmidtke, Peter;
Bidon-Chanal, Axel;
Luque, F. Javier;
Barril, Xavier

Publication type:

Article

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

Published in:

Journal of Computational Chemistry, 2009, v. 30, n. 4, p. 601, doi. 10.1002/jcc.21087

By:

BUTLER, KEITH T.;
LUQUE, F. JAVIER;
BARRIL, XAVIER

Publication type:

Article

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

Published in:

Journal of Computational Chemistry, 2008, v. 29, n. 4, p. 578, doi. 10.1002/jcc.20814

By:

Forti, Flavio;
Barril, Xavier;
Luque, F. Javier;
Orozco, Modesto

Publication type:

Article

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

Published in:

Proteins, 2012, v. 80, n. 1, p. 269, doi. 10.1002/prot.23205

By:

Seco, Jesus;
Ferrer-Costa, Carles;
Campanera, Josep M.;
Soliva, Robert;
Barril, Xavier

Publication type:

Article

An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder.

Published in:

Communications Chemistry, 2019, v. 2, n. 1, p. N.PAG, doi. 10.1038/s42004-019-0205-5

By:

Majewski, Maciej;
Ruiz-Carmona, Sergio;
Barril, Xavier

Publication type:

Article

Front Cover: DUckCov: a Dynamic Undocking‐Based Virtual Screening Protocol for Covalent Binders (ChemMedChem 10/2019).

Published in:

ChemMedChem, 2019, v. 14, n. 10, p. 994, doi. 10.1002/cmdc.201900263

By:

Rachman, Moira;
Scarpino, Andrea;
Bajusz, Dávid;
Pálfy, Gyula;
Vida, István;
Perczel, András;
Barril, Xavier;
Keserű, György M.

Publication type:

Article

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

Published in:

ChemMedChem, 2019, v. 14, n. 10, p. 1011, doi. 10.1002/cmdc.201900078

By:

Rachman, Moira;
Scarpino, Andrea;
Bajusz, Dávid;
Pálfy, Gyula;
Vida, István;
Perczel, András;
Barril, Xavier;
Keserű, György M.

Publication type:

Article

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

Published in:

ChemMedChem, 2016, v. 11, n. 8, p. 928, doi. 10.1002/cmdc.201500467

By:

Bayó‐Puxan, Núria;
Rodríguez‐Mias, Ricard;
Goldflam, Michael;
Kotev, Martin;
Ciudad, Sonia;
Hipolito, Christopher J.;
Varese, Monica;
Suga, Hiroaki;
Campos‐Olivas, Ramón;
Barril, Xavier;
Guallar, Víctor;
Teixidó, Meritxell;
García, Jesús;
Giralt, Ernest

Publication type:

Article

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 4, p. 1, doi. 10.1371/journal.pcbi.1003571

By:

Ruiz-Carmona, Sergio;
Alvarez-Garcia, Daniel;
Foloppe, Nicolas;
Garmendia-Doval, A. Beatriz;
Juhos, Szilveszter;
Schmidtke, Peter;
Barril, Xavier;
Hubbard, Roderick E.;
Morley, S. David

Publication type:

Article

VAV3 mediates resistance to breast cancer endocrine therapy.

Published in:

Breast Cancer Research, 2014, v. 16, n. 3, p. 1, doi. 10.1186/bcr3664

By:

Aguilar, Helena;
Urruticoechea, Ander;
Halonen, Pasi;
Kiyotani, Kazuma;
Mushiroda, Taisei;
Barril, Xavier;
Serra-Musach, Jordi;
Islam, Abul;
Caizzi, Livia;
Croce, Luciano Di;
Nevedomskaya, Ekaterina;
Zwart, Wilbert;
Bostner, Josefine;
Karlsson, Elin;
Tenorio, Gizeh Pérez;
Fornander, Tommy;
Sgroi, Dennis C.;
Garcia-Mata, Rafael;
Jansen, Maurice P.H.M.;
García, Nadia

Publication type:

Article

VAV3 mediates resistance to breast cancer endocrine therapy.

Published in:

2014

By:

Aguilar, Helena;
Urruticoechea, Ander;
Halonen, Pasi;
Kiyotani, Kazuma;
Mushiroda, Taisei;
Barril, Xavier;
Serra-Musach, Jordi;
Islam, Abul;
Caizzi, Livia;
Di Croce, Luciano;
Nevedomskaya, Ekaterina;
Zwart, Wilbert;
Bostner, Josefine;
Karlsson, Elin;
Pérez Tenorio, Gizeh;
Fornander, Tommy;
Sgroi, Dennis C;
Garcia-Mata, Rafael;
Jansen, Maurice Phm;
García, Nadia

Publication type:

journal article

Discovery of allosteric regulators with clinical potential to stabilize alpha-L-iduronidase in mucopolysaccharidosis type I.

Published in:

PLoS ONE, 2024, v. 19, n. 5, p. 1, doi. 10.1371/journal.pone.0303789

By:

Cubero, Elena;
Ruano, Ana;
Delgado, Aida;
Barril, Xavier;
Morales, Sara;
Trapero, Ana;
Leoni, Lorenzo;
Bellotto, Manolo;
Maj, Roberto;
Guzmán, Beatriz Calvo-Flores;
Pérez-Carmona, Natalia;
Garcia-Collazo, Ana Maria

Publication type:

Article

Validation of a highly sensitive HaloTag-based assay to evaluate the potency of a novel class of allosteric β-Galactosidase correctors.

Published in:

PLoS ONE, 2023, v. 18, n. 11, p. 1, doi. 10.1371/journal.pone.0294437

By:

Rudinskiy, Mikhail;
Pons-Vizcarra, Maria;
Soldà, Tatiana;
Fregno, Ilaria;
Bergmann, Timothy Jan;
Ruano, Ana;
Delgado, Aida;
Morales, Sara;
Barril, Xavier;
Bellotto, Manolo;
Cubero, Elena;
García-Collazo, Ana María;
Pérez-Carmona, Natalia;
Molinari, Maurizio

Publication type:

Article

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

Published in:

2017

By:

Barril, Xavier

Publication type:

Editorial

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

Published in:

Expert Opinion on Drug Discovery, 2006, v. 1, n. 4, p. 335, doi. 10.1517/17460441.1.4.335

By:

Barril, Xavier;
Fradera, Xavier

Publication type:

Article

Testing automatic methods to predict free binding energy of host–guest complexes in SAMPL7 challenge.

Published in:

Journal of Computer-Aided Molecular Design, 2021, v. 35, n. 2, p. 209, doi. 10.1007/s10822-020-00370-6

By:

Serillon, Dylan;
Bo, Carles;
Barril, Xavier

Publication type:

Article

TuberQ: a Mycobacterium tuberculosis protein druggability database.

Published in:

Database: The Journal of Biological Databases & Curation, 2014, v. 2014, p. 1, doi. 10.1093/database/bau035

By:

Radusky, Leandro;
Defelipe, Lucas A.;
Lanzarotti, Esteban;
Luque, Javier;
Barril, Xavier;
Marti, Marcelo A.;
Turjanski, Adrián G.

Publication type:

Article

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.

Published in:

PLoS ONE, 2015, v. 10, n. 7, p. 1, doi. 10.1371/journal.pone.0131462

By:

Estupiñán, Mónica;
Álvarez-García, Daniel;
Barril, Xavier;
Diaz, Pilar;
Manresa, Angeles

Publication type:

Article

The Role of Water Networks in Phosphodiesterase Inhibitor Dissociation and Kinetic Selectivity.

Published in:

ChemMedChem, 2024, v. 19, n. 22, p. 1, doi. 10.1002/cmdc.202400417

By:

Blaazer, Antoni R.;
Singh, Abhimanyu K.;
Zara, Lorena;
Boronat, Pierre;
Bautista, Lady J.;
Irving, Steve;
Majewski, Maciej;
Barril, Xavier;
Wijtmans, Maikel;
Danielson, U. Helena;
Sterk, Geert Jan;
Leurs, Rob;
van Muijlwijk‐Koezen, Jacqueline E.;
Brown, David G.;
de Esch, Iwan J. P.

Publication type:

Article

On the transferability of fractional contributions to the hydration free energy of amino acids.

Published in:

Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2013, v. 132, n. 3, p. 1, doi. 10.1007/s00214-013-1343-y

By:

Campanera, Josep;
Barril, Xavier;
Luque, F.

Publication type:

Article

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

Published in:

Molecules, 2018, v. 23, n. 12, p. 3269, doi. 10.3390/molecules23123269

By:

Defelipe, Lucas A.;
Arcon, Juan Pablo;
Modenutti, Carlos P.;
Marti, Marcelo A.;
Turjanski, Adrián G.;
Barril, Xavier;
Wade, Rebecca;
Salo-Ahen, Outi

Publication type:

Article