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Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites

Journal of medicinal chemistry, 2010-08, Vol.53 (15), p.5858-5867

2010

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

PLoS computational biology, 2014-04, Vol.10 (4), p.e1003571-e1003571

2014

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

Bioinformatics, 2021-06, Vol.37 (10), p.1376-1382

2021

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

Bioinformatics, 2011-12, Vol.27 (23), p.3276-3285

2011

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

Journal of chemical theory and computation, 2014-06, Vol.10 (6), p.2608-2614

2014

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

Journal of computer-aided molecular design, 2021-02, Vol.35 (2), p.209-222

2021

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Detecting similar binding pockets to enable systems polypharmacology

PLoS computational biology, 2017-06, Vol.13 (6), p.e1005522-e1005522

2017

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

Communications chemistry, 2019-09, Vol.2 (1), Article 110

2019

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

PloS one, 2024-05, Vol.19 (5), p.e0303789-e0303789

2024

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Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures

Journal of medicinal chemistry, 2005-06, Vol.48 (13), p.4432-4443

2005

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

PloS one, 2023-11, Vol.18 (11), p.e0294437-e0294437

2023

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

Journal of chemical information and modeling, 2017-04, Vol.57 (4), p.846-863

2017

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Development of an Automatic Pipeline for Participation in the CELPP Challenge

International journal of molecular sciences, 2022-04, Vol.23 (9), p.4756

2022

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Cosolvent-Based Protein Pharmacophore for Ligand Enrichment in Virtual Screening

Journal of chemical information and modeling, 2019-08, Vol.59 (8), p.3572-3583

2019

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Solvents to Fragments to Drugs: MD Applications in Drug Design

Molecules (Basel, Switzerland), 2018-12, Vol.23 (12), p.3269

2018

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Protein flexibility and ligand recognition: challenges for molecular modeling

Current topics in medicinal chemistry, 2011, Vol.11 (2), p.192

2011

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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

PloS one, 2015-07, Vol.10 (7), p.e0131462-e0131462

2015

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Improvements in docking scoring functions: the physics-based perspective

Journal of cheminformatics, 2012-05, Vol.4 (Suppl 1), p.O22-O22, Article O22

Barril, Xavier

2012

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Tacripyrines, the First Tacrine−Dihydropyridine Hybrids, as Multitarget-Directed Ligands for the Treatment of Alzheimer’s Disease

Journal of medicinal chemistry, 2009-05, Vol.52 (9), p.2724-2732

2009

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Structural Stability Predicts the Binding Mode of Protein–Ligand Complexes

Journal of chemical information and modeling, 2020-03, Vol.60 (3), p.1644-1651

2020

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Novel, Potent Small-Molecule Inhibitors of the Molecular Chaperone Hsp90 Discovered through Structure-Based Design

Journal of medicinal chemistry, 2005-06, Vol.48 (13), p.4212-4215

2005

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Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites

Journal of medicinal chemistry, 2014-10, Vol.57 (20), p.8530-8539

2014

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Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites

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

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

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

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

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

Detecting similar binding pockets to enable systems polypharmacology

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

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

Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures

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

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

Development of an Automatic Pipeline for Participation in the CELPP Challenge

Cosolvent-Based Protein Pharmacophore for Ligand Enrichment in Virtual Screening

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

Solvents to Fragments to Drugs: MD Applications in Drug Design

4,5-Diarylisoxazole Hsp90 Chaperone Inhibitors: Potential Therapeutic Agents for the Treatment of Cancer

Protein flexibility and ligand recognition: challenges for molecular modeling

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

Improvements in docking scoring functions: the physics-based perspective

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

Tacripyrines, the First Tacrine−Dihydropyridine Hybrids, as Multitarget-Directed Ligands for the Treatment of Alzheimer’s Disease

Structural Stability Predicts the Binding Mode of Protein–Ligand Complexes

Novel, Potent Small-Molecule Inhibitors of the Molecular Chaperone Hsp90 Discovered through Structure-Based Design

Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites

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