X. Barril

发表

Salt bridge interactions: Stability of the ionic and neutral complexes in the gas phase, in solution, and in proteins

F. J. Luque, X. Barril, C. Alemán, 1998, Proteins.

In Silico Screening

F. J. Luque, X. Barril, F. Luque, 2010 .

Incorporating protein flexibility into docking and structure-based drug design

X. Barril, X. Fradera, 2006, Expert opinion on drug discovery.

Molecular modelling.

Xavier Barril, Robert Soliva, X. Barril, 2006, Molecular bioSystems.

Structure-based discovery of a new class of Hsp90 inhibitors.

X. Barril, M. Drysdale, R. Hubbard, 2005, Bioorganic & medicinal chemistry letters.

Solvents to Fragments to Drugs: MD Applications in Drug Design

Juan Pablo Arcon, Carlos P. Modenutti, X. Barril, 2018, Molecules.

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

X. Barril, P. Schmidtke, Peter Schmidtke, 2010, Journal of medicinal chemistry.

Structure-activity relationships in purine-based inhibitor binding to HSP90 isoforms.

X. Barril, M. Drysdale, P. Workman, 2004, Chemistry & biology.

Virtual screening in structure-based drug discovery.

X. Barril, R. Hubbard, S. D. Morley, 2004, Mini reviews in medicinal chemistry.

Unveiling the full potential of flexible receptor docking using multiple crystallographic structures.

X. Barril, S. D. Morley, 2005, Journal of medicinal chemistry.

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.

X. Barril, B. Davis, M. Drysdale, 2009, Journal of medicinal chemistry.

Binding site detection and druggability index from first principles.

F. J. Luque, X. Barril, Jesus Seco, 2009, Journal of medicinal chemistry.

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

F. J. Luque, X. Barril, J. Murray, 2011, Journal of the American Chemical Society.

Protein flexibility and ligand recognition: challenges for molecular modeling.

F. J. Luque, X. Barril, F. Spyrakis, 2011, Current topics in medicinal chemistry.

Ligand discovery: Docking points.

X. Barril, 2014, Nature chemistry.

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

X. Barril, Daniel Alvarez-Garcia, 2014, Journal of medicinal chemistry.

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

F. J. Luque, X. Barril, B. Davis, 2016, Nature Chemistry.

Druggability predictions: methods, limitations, and applications

X. Barril, 2013 .

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

F. J. Luque, X. Barril, M. Orozco, 2015, The journal of physical chemistry. B.

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

Mike Wood, Brian Dymock, Xavier Barril, 2007, Journal of medicinal chemistry.

VAV3 mediates resistance to breast cancer endocrine therapy

F. Climent, Yusuke Nakamura, M. Esteller, 2014, Breast Cancer Research.

Binding of calix[4]pyrroles to pyridine N-oxides probed with surface plasmon resonance

X. Barril, P. Ballester, C. O’Sullivan, 2014 .

Computational Design of Inhibitors Targeting the Catalytic β Subunit of Escherichia coli FOF1-ATP Synthase

X. Barril, Y. B. Ruiz-Blanco, E. García-Hernández, 2022, Antibiotics.

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

L. Pearl, X. Barril, M. Drysdale, 2008, Cancer research.

Novel, potent small-molecule inhibitors of the molecular chaperone Hsp90 discovered through structure-based design.

Xavier Barril, Paul Workman, Roderick E Hubbard, 2005, Journal of medicinal chemistry.

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

X. Barril, Sergio Ruiz-Carmona, Maciej Majewski, 2019, Communications Chemistry.

Pharmacological chaperones for enzyme enhancement therapy in genetic diseases.

Xavier Barril, Marc Martinell, Juan Aymami, 2013, Pharmaceutical patent analyst.

Partitioning of Free Energies of Solvation into Fragment Contributions: Applications in Drug Design

Xavier Barril, F. J. Luque, Modesto Orozco, 2001 .

Simplified descriptions of the topological distribution of hydrophilic/hydrophobic characteristics of molecules

F. Javier Luque, Xavier Barril, F. J. Luque, 2000 .

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

F. J. Luque, X. Barril, J. Campanera, 2013, Theoretical Chemistry Accounts.

Chapter 4 - Nucleic Acid Bases in Solution

F. J. Luque, X. Barril, M. Orozco, 1999 .

Predicting relative binding free energies of tacrine-huperzine A hybrids as inhibitors of acetylcholinesterase.

F. J. Luque, X. Barril, M. Orozco, 1999, Journal of medicinal chemistry.

Fluorogenic Trp(redBODIPY) cyclopeptide targeting keratin 1 for imaging of aggressive carcinomas†

X. Barril, M. Vendrell, Binzhi Qian, 2019, Chemical science.

On the Use of SCRF Methods in Drug Design Studies

F. J. Luque, X. Barril, M. Orozco, 2000 .

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

X. Barril, 2017, Expert opinion on drug discovery.

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

X. Barril, M. Drysdale, P. Workman, 2005, Bioorganic & medicinal chemistry letters.

Cosolvent Sites-Based Discovery of Mycobacterium Tuberculosis Protein Kinase G Inhibitors

Elias D. López, X. Barril, A. Turjanski, 2022, Journal of medicinal chemistry.

Revealing 2-dimethylhydrazino-2-alkyl alkynyl sphingosine derivatives as sphingosine kinase 2 inhibitors: Some hints on the structural basis for selective inhibition.

X. Barril, R. Beltrán-Debón, M. Sanz, 2022, Bioorganic chemistry.

Discovery of a novel kinase hinge binder fragment by dynamic undocking

X. Barril, L. Buday, G. Keserű, 2020, RSC medicinal chemistry.

Rational design of reversible acetylcholinesterase inhibitors.

F. J. Luque, X. Barril, M. Orozco, 2002, Mini reviews in medicinal chemistry.

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

Xavier Barril, Nicolas Foloppe, Daniel Alvarez-Garcia, 2014, PLoS Comput. Biol..

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

Xavier Barril, F. J. Luque, F Javier Luque, 2009, Journal of medicinal chemistry.

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

F. J. Luque, X. Barril, R. León, 2008, Bioorganic & medicinal chemistry.

4-Amino derivatives of the Hsp90 inhibitor CCT018159.

Xavier Barril, Paul Workman, Allan M Jordan, 2006, Bioorganic & medicinal chemistry letters.

Synthesis, in vitro pharmacology, and molecular modeling of syn-huprines as acetylcholinesterase inhibitors.

F. J. Luque, X. Barril, M. Orozco, 2001, Journal of medicinal chemistry.

New tacrine-huperzine A hybrids (huprines): highly potent tight-binding acetylcholinesterase inhibitors of interest for the treatment of Alzheimer's disease.

F. J. Luque, J E Baños, X. Barril, 2000, Journal of medicinal chemistry.

Luque, Francisco Javier Synthesis, in Vitro Pharmacology, and Molecular Modeling of Very Potent Tacrine−Huperzine A Hybrids as Acetylcholinesterase Inhibitors of Potential Interest for the Treatment of Alzheimer's Disease

F. J. Luque, X. Barril, M. Orozco, 2021 .

Synthesis, in vitro pharmacology, and molecular modeling of very potent tacrine-huperzine A hybrids as acetylcholinesterase inhibitors of potential interest for the treatment of Alzheimer's disease.

F. J. Luque, X. Barril, M. Orozco, 1999, Journal of medicinal chemistry.

Towards improved acetylcholinesterase inhibitors: a structural and computational approach.

F. J. Luque, X. Barril, M. Orozco, 2001, Mini reviews in medicinal chemistry.

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

X. Barril, M. Goldflam, E. Giralt, 2015, ChemMedChem.

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

X. Barril, P. Díaz, Daniel Alvarez-Garcia, 2015, PloS one.

Inherent conformational flexibility of F1-ATPase α-subunit.

X. Barril, E. García-Hernández, Otto Hahn-Herrera, 2016, Biochimica et biophysica acta.

Fragment-to-lead tailored in silico design

Xavier Barril, Moira Rachman, Maciej Majewski, 2021, Drug Discovery Today: Technologies.

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

F. Javier Luque, Xavier Barril, F. J. Luque, 2011, Bioinform..

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

X. Barril, R. Soliva, C. Ferrer-Costa, 2012, Proteins.

Adenine derived inhibitors of the molecular chaperone HSP90-SAR explained through multiple X-ray structures.

Brian Dymock, Xavier Barril, Roderick E Hubbard, 2004, Bioorganic & medicinal chemistry letters.

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

Xavier Barril, Yvonne Westermaier, Leonardo Scapozza, 2015, Methods.

Conformational landscape of small ligands: a multilevel strategy to determine the conformational penalty of bioactive ligands

F. Javier Luque, Xavier Barril, F. J. Luque, 2015 .

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

Claudio N. Cavasotto, Claudio N Cavasotto, Xavier Barril, 2012, Journal of chemical theory and computation.

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

Xavier Barril, Norberto Sánchez-Cruz, José L Medina-Franco, 2020, Bioinform..

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

Xavier Barril, Daniel Alvarez-Garcia, X. Barril, 2014, Journal of chemical theory and computation.

A fluorescence polarization assay for inhibitors of Hsp90.

X. Barril, M. Drysdale, P. Workman, 2006, Analytical biochemistry.

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

F. J. Luque, J L Gelpí, X. Barril, 2001, Proteins.

Are protein-ligand complexes robust structures?

Xavier Barril, Sergio Ruiz-Carmona, Maciej Majewski, 2018, bioRxiv.

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

Xavier Barril, Marcelo A. Marti, Adrian Gustavo Turjanski, 2017, J. Chem. Inf. Model..

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

L. Pearl, X. Barril, M. Drysdale, 2007, Molecular Cancer Therapeutics.

Design and Characterization of Libraries of Molecular Fragments for Use in NMR Screening against Protein Targets

Brian Dymock, Xavier Barril, Fareed Aboul-Ela, 2004, J. Chem. Inf. Model..

A hydrophobic similarity analysis of solvation effects on nucleic acid bases

Xavier Barril, F. J. Luque, Modesto Orozco, 2007, Journal of molecular modeling.

Predicting how drug molecules bind to their protein targets.

Xavier Barril, Roderick E Hubbard, X. Barril, 2018, Current opinion in pharmacology.

Multi-Responsive Eight-State Bis(acridinium-Zn(II) porphyrin) Receptor

X. Barril, N. Armaroli, B. Ventura, 2023, Journal of the American Chemical Society.

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

X. Barril, J. Boutin, P. Ducrot, 2017, Journal of Computer-Aided Molecular Design.

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

X. Barril, C. Estarellas, A. Bidon-Chanal, 2017, Molecular pharmaceutics.

TuberQ: a Mycobacterium tuberculosis protein druggability database

F. Javier Luque, Xavier Barril, F. J. Luque, 2014, Database J. Biol. Databases Curation.

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

F. Javier Luque, Xavier Barril, F. J. Luque, 2008, J. Comput. Chem..

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

Maciej Majewski, Xavier Barril, Sergio Ruiz-Carmona, 2018, Methods in molecular biology.

3D structure of Torpedo californica acetylcholinesterase complexed with huprine X at 2.1 A resolution: kinetic and molecular dynamic correlates.

F. J. Luque, J L Sussman, I Silman, 2002, Biochemistry.

Discovery of Novel BRD4 Ligand Scaffolds by Automated Navigation of the Fragment Chemical Space.

X. Barril, F. von Delft, P. Filippakopoulos, 2021, Journal of medicinal chemistry.

Theoretical Methods for the Representation of Solvent

F. J. Luque, X. Barril, M. Orozco, 1996 .

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

Dávid Bajusz, András Perczel, Moira Rachman, 2019, ChemMedChem.

Molecular simulation methods in drug discovery: a prospective outlook

F. Javier Luque, Xavier Barril, F. J. Luque, 2011, Journal of Computer-Aided Molecular Design.

Docking-undocking combination applied to the D3R Grand Challenge 2015

Xavier Barril, Sergio Ruiz-Carmona, X. Barril, 2016, Journal of Computer-Aided Molecular Design.

Development of an Automatic Pipeline for Participation in the CELPP Challenge

X. Barril, P. Schmidtke, Daniel Alvarez-Garcia, 2022, International journal of molecular sciences.

Targeting Novel Allosteric Sites with Confidence: Methods and Applications

Xavier Barril, X. Barril, 2019, Proceedings.

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

X. Barril, P. Schmidtke, Daniel Alvarez-Garcia, 2022 .

Enzyme Enhancement Therapy through non-competitive pharmacological chaperones

Xavier Barril, Marc Martinell, Katsumi Higaki, 2014, IWBBIO.

Transferability of fragmental contributions to the octanol/water partition coefficient: An NDDO‐based MST study

F. Javier Luque, Xavier Barril, F. J. Luque, 2003, J. Comput. Chem..

Structural Stability Predicts the Binding Mode of Protein-Ligand Complexes

Maciej Majewski, Xavier Barril, X. Barril, 2020, J. Chem. Inf. Model..

Toward accurate relative energy predictions of the bioactive conformation of drugs

Keith T. Butler, F. Javier Luque, Xavier Barril, 2009, J. Comput. Chem..

Lenalidomide Stabilizes Protein–Protein Complexes by Turning Labile Intermolecular H-Bonds into Robust Interactions

X. Barril, J. Juárez-Jiménez, Marina Miñarro-Lleonar, 2023, Journal of medicinal chemistry.

Eytan Ruppin, Xavier Barril, Gabriele Cruciani, 2017, PLoS Comput. Biol..

Cosolvent-Based Protein Pharmacophore for Ligand Enrichment in Virtual Screening

Xavier Barril, Adrian Gustavo Turjanski, Osvaldo Burastero, 2019, J. Chem. Inf. Model..

How accurate can molecular dynamics/linear response and Poisson–Boltzmann/solvent accessible surface calculations be for predicting relative binding affinities? Acetylcholinesterase huprine inhibitors as a test case

M. Orozco, X. Barril, M. Orozco, 2001 .

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

X. Barril, C. Bo, Dylan Serillon, 2021, Journal of Computer-Aided Molecular Design.

Ensemble Docking from Homology Models.

Xavier Barril, Modesto Orozco, Eva Maria Novoa, 2010, Journal of chemical theory and computation.

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

Ana Maria Garcia-Collazo, X. Barril, M. Molinari, 2023, PloS one.

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

X. Barril, E. Cubero, Peter Schmidtke, 2021, Current drug discovery technologies.

Fractional description of free energies of solvation

F. Javier Luque, Xavier Barril, Modesto Orozco, 1999, J. Comput. Aided Mol. Des..

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

X. Barril, B. Davis, J. Murray, 2016, Nature Chemistry.