Computational chemistry in drug lead discovery and design

Structure-based drug design for envelope protein E2 uncovers a new class of bovine viral diarrhea inhibitors that block virus entry

(2018) María José Pascual et al.   ANTIVIRAL RESEARCH

Decoys Selection in Benchmarking Datasets: Overview and Perspectives

(2018) Manon Réau et al.   Frontiers in Pharmacology

Discovery of Novel Bovine Viral Diarrhea Inhibitors Using Structure-Based Virtual Screening on the Envelope Protein E2

(2018) Mariela Bollini et al.   Frontiers in Chemistry

Quantum Chemical Approaches in Structure-Based Virtual Screening and Lead Optimization

(2018) Claudio N. Cavasotto et al.   Frontiers in Chemistry

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2017) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Correction: An Exact Expression to Calculate the Derivatives of Position-Dependent Observables in Molecular Simulations with Flexible Constraints

(2017) Pablo Echenique et al.   PLoS One

Investigating molecular dynamics-guided lead optimization of EGFR inhibitors

(2016) Martin J. Lavecchia et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

(2016) Ulf Ryde et al.   CHEMICAL REVIEWS

Prospects of Applying Enhanced Semi-Empirical QM Methods for 2101 Virtual Drug Design

(2016) Nusret Duygu Yilmazer et al.   CURRENT MEDICINAL CHEMISTRY

Structural Diversity of Ligand-Binding Androgen Receptors Revealed by Microsecond Long Molecular Dynamics Simulations and Enhanced Sampling

(2016) Mojie Duan et al.   Journal of Chemical Theory and Computation

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

(2016) Symon Gathiaka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description

(2015) Francesca Spyrakis et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models

(2015) Claudio N. Cavasotto et al.   CHEMICAL COMMUNICATIONS

Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives

(2015) Nathalie Lagarde et al.   Journal of Chemical Information and Modeling

Improvements, trends, and new ideas in molecular docking: 2012-2013 in review

(2015) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Interaction mechanism exploration of R-bicalutamide/S-1 with WT/W741L AR using molecular dynamics simulations

(2015) Hongli Liu et al.   Molecular BioSystems

Methods for Docking Small Molecules to Macromolecules: A User’s Perspective. 1. The Theory

(2014) Nathanael Weill et al.   CURRENT PHARMACEUTICAL DESIGN

Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges

(2014) Irina Kufareva et al.   STRUCTURE

High throughput screening for inhibitors of the HECT ubiquitin E3 ligase ITCH identifies antidepressant drugs as regulators of autophagy

(2014) M Rossi et al.   Cell Death & Disease

Mastering tricyclic ring systems for desirable functional cannabinoid activity

(2013) Ravil R. Petrov et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

The application of quantum mechanics in structure-based drug design

(2013) Daniel Mucs et al.   Expert Opinion on Drug Discovery

The Histidine-Phosphocarrier Protein of the Phosphoenolpyruvate: Sugar Phosphotransferase System of Bacillus sphaericus Self-Associates

(2013) Rosa Doménech et al.   PLoS One

Challenges for Academic Drug Discovery

(2012) William L. Jorgensen   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

X-Aptamers: A Bead-Based Selection Method for Random Incorporation of Druglike Moieties onto Next-Generation Aptamers for Enhanced Binding

(2012) Weiguo He et al.   BIOCHEMISTRY

Protein Flexibility and Ligand Recognition: Challenges for Molecular Modeling

(2012) Francesca Spyrakis et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

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

(2012) Flavio Forti et al.   Journal of Chemical Theory and Computation

New insights from structural biology into the druggability of G protein-coupled receptors

(2012) Jonathan S. Mason et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Homology Models in Docking and High-Throughput Docking

(2011) Claudio N. Cavasotto   CURRENT TOPICS IN MEDICINAL CHEMISTRY

The canonical equilibrium of constrained molecular models

(2011) P. Echenique et al.   European Physical Journal-Special Topics

Ligand and Decoy Sets for Docking to G Protein-Coupled Receptors

(2011) Edgar A. Gatica et al.   Journal of Chemical Information and Modeling

Virtual Decoy Sets for Molecular Docking Benchmarks

(2011) Izhar Wallach et al.   Journal of Chemical Information and Modeling

Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain

(2011) Victor M. Anisimov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1

(2011) Victor M. Anisimov et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Hydration Free Energies Using Semiempirical Quantum Mechanical Hamiltonians and a Continuum Solvent Model with Multiple Atomic-Type Parameters

(2011) Victor M. Anisimov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Significance of G Protein-Coupled Receptor Crystallography for Drug Discovery

(2011) J. A. Salon et al.   PHARMACOLOGICAL REVIEWS

Rationally Designed Interfacial Peptides Are Efficient In Vitro Inhibitors of HIV-1 Capsid Assembly with Antiviral Activity

(2011) Rebeca Bocanegra et al.   PLoS One

An Exact Expression to Calculate the Derivatives of Position-Dependent Observables in Molecular Simulations with Flexible Constraints

(2011) Pablo Echenique et al.   PLoS One

Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment

(2011) Irina Kufareva et al.   STRUCTURE

Outstanding challenges in protein-ligand docking and structure-based virtual screening

(2011) Bohdan Waszkowycz et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis

(2010) Olivier Sperandio et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Tackling the challenges posed by target flexibility in drug design

(2010) Christian Beier et al.   Expert Opinion on Drug Discovery

Ligand-Steered Modeling and Docking: A Benchmarking Study in Class A G-Protein-Coupled Receptors

(2010) Sharangdhar S. Phatak et al.   Journal of Chemical Information and Modeling

Rapid Context-Dependent Ligand Desolvation in Molecular Docking

(2010) Michael M. Mysinger et al.   Journal of Chemical Information and Modeling

Docking-based virtual screening for ligands of G protein-coupled receptors: Not only crystal structures but also in silico models

(2010) Santiago Vilar et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

cAMP-dependent protein kinase: Crystallographic insights into substrate recognition and phosphotransfer

(2010) Madhusudan et al.   PROTEIN SCIENCE

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

2,3-Dihydro-1-Benzofuran Derivatives as a Series of Potent Selective Cannabinoid Receptor 2 Agonists: Design, Synthesis, and Binding Mode Prediction through Ligand-Steered Modeling

(2009) Philippe Diaz et al.   ChemMedChem

Quantum Mechanical Dynamics of Charge Transfer in Ubiquitin in Aqueous Solution

(2009) Victor M. Anisimov et al.   CHEMPHYSCHEM

Structure-Based Virtual Ligand Screening: Recent Success Stories

(2009) Bruno Villoutreix et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Homology modeling in drug discovery: current trends and applications

(2009) Claudio N. Cavasotto et al.   DRUG DISCOVERY TODAY

High-throughput andin silicoscreenings in drug discovery

(2009) Sharangdhar S Phatak et al.   Expert Opinion on Drug Discovery

Molecular Modeling of Glucose Diffusivity in Silica Nanochannels

(2009) Arturas Ziemys et al.   JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY

What recent ribosome structures have revealed about the mechanism of translation

(2009) T. Martin Schmeing et al.   NATURE

Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008

(2009) Mayako Michino et al.   NATURE REVIEWS DRUG DISCOVERY

DOCK 6: Combining techniques to model RNA-small molecule complexes

(2009) P. T. Lang et al.   RNA

The Binding Mode of Petrosaspongiolide M to the Human Group IIA Phospholipase A2: Exploring the Role of Covalent and Noncovalent Interactions in the Inhibition Process

(2008) Maria Chiara Monti et al.   CHEMISTRY-A EUROPEAN JOURNAL

Docking and High Throughput Docking: Successes and the Challenge of Protein Flexibility

(2008) Claudio Cavasotto et al.   Current Computer-Aided Drug Design

Cross-Docking of Inhibitors into CDK2 Structures. 2

(2008) Johannes H. Voigt et al.   Journal of Chemical Information and Modeling

Community benchmarks for virtual screening

(2008) John J. Irwin   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking

(2008) Andreas May et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Novel Chemotypes to a G-Protein-Coupled Receptor through Ligand-Steered Homology Modeling and Structure-Based Virtual Screening

(2008) Claudio N. Cavasotto et al.   JOURNAL OF MEDICINAL CHEMISTRY

Target Flexibility: An Emerging Consideration in Drug Discovery and Design†

(2008) Pietro Cozzini et al.   JOURNAL OF MEDICINAL CHEMISTRY

6-Methoxy-N-alkyl Isatin Acylhydrazone Derivatives as a Novel Series of Potent Selective Cannabinoid Receptor 2 Inverse Agonists: Design, Synthesis, and Binding Mode Prediction

(2008) Philippe Diaz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Molecular basis of agonicity and antagonicity in the androgen receptor studied by molecular dynamics simulations

(2008) William H. Bisson et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Phosphorylation of Liver X Receptor   Selectively Regulates Target Gene Expression in Macrophages

(2008) I. P. Torra et al.   MOLECULAR AND CELLULAR BIOLOGY

Glucocorticoid Receptor Phosphorylation Differentially Affects Target Gene Expression

(2008) Weiwei Chen et al.   MOLECULAR ENDOCRINOLOGY

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Structural diversity of G protein-coupled receptors and significance for drug discovery

(2008) Malin C. Lagerström et al.   NATURE REVIEWS DRUG DISCOVERY

MODBASE, a database of annotated comparative protein structure models and associated resources

(2008) U. Pieper et al.   NUCLEIC ACIDS RESEARCH