Exploiting computationally derived out-of-the-box protein conformations for drug design

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

(2016) Guanghong Wei et al.   CHEMICAL REVIEWS

Drugging specific conformational states of GPCRs: challenges and opportunities for computational chemistry

(2016) Maria Martí-Solano et al.   DRUG DISCOVERY TODAY

Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2

(2016) Pasquale Pisani et al.   PLoS One

Allostery without a conformational change? Revisiting the paradigm

(2015) Ruth Nussinov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

G Protein-Coupled Receptors: Dynamic Machines for Signaling Pain and Itch

(2015) Pierangelo Geppetti et al.   NEURON

Exploring the Alzheimer amyloid-β peptide conformational ensemble: A review of molecular dynamics approaches

(2015) Linh Tran et al.   PEPTIDES

Discovery of multiple hidden allosteric sites by combining Markov state models and experiments

(2015) Gregory R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure-based discovery of the first allosteric inhibitors of cyclin-dependent kinase 2

(2014) Giulio Rastelli et al.   CELL CYCLE

Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances

(2014) Evanthia Lionta et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Structure-based design of small-molecule protein–protein interaction modulators: the story so far

(2014) Federico Falchi et al.   Future Medicinal Chemistry

Exploring Protein Kinase Conformation Using Swarm-Enhanced Sampling Molecular Dynamics

(2014) Alessio Atzori et al.   Journal of Chemical Information and Modeling

Activation pathway of Src kinase reveals intermediate states as targets for drug design

(2014) Diwakar Shukla et al.   Nature Communications

Microsecond molecular dynamics simulation of Aβ42 and identification of a novel dual inhibitor of Aβ42 aggregation and BACE1 activity

(2013) Yuan-yuan Wang et al.   ACTA PHARMACOLOGICA SINICA

Structural characterization of the cyclin-dependent protein kinase family

(2013) Jane A. Endicott et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics

(2013) Hongtao Zhao et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Allostery in Disease and in Drug Discovery

(2013) Ruth Nussinov et al.   CELL

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

CURRENT PROGRESS IN STRUCTURE-BASED RATIONAL DRUG DESIGN MARKS A NEW MINDSET IN DRUG DISCOVERY

(2013) Valère Lounnas et al.   Computational and Structural Biotechnology Journal

Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review

(2012) Tiejun Cheng et al.   AAPS Journal

Structure-Function of the G Protein–Coupled Receptor Superfamily

(2012) Vsevolod Katritch et al.   Annual Review of Pharmacology and Toxicology

Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer

(2012) Yu-Shan Lin et al.   BIOPHYSICAL JOURNAL

Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design

(2012) William Sinko et al.   Chemical Biology & Drug Design

Discovery of Tyrosine Kinase Inhibitors by Docking into an Inactive Kinase Conformation Generated by Molecular Dynamics

(2012) Hongtao Zhao et al.   ChemMedChem

αC helix displacement as a general approach for allosteric modulation of protein kinases

(2012) Lorenzo Palmieri et al.   DRUG DISCOVERY TODAY

Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations

(2012) Miriam Sgobba et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Virtual compound screening in drug discovery

(2012) Dagmar Stumpfe et al.   Future Medicinal Chemistry

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

A new era of GPCR structural and chemical biology

(2012) Sébastien Granier et al.   Nature Chemical Biology

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

(2012) G. R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Motions as a Drug Target: Mechanistic Simulations of Anthrax Toxin Edema Factor Function Led to the Discovery of Novel Allosteric Inhibitors

(2012) Élodie Laine et al.   Toxins

Discovery of a Potential Allosteric Ligand Binding Site in CDK2

(2011) Stephane Betzi et al.   ACS Chemical Biology

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

(2011) Peter Schmidtke et al.   BIOINFORMATICS

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

(2011) Kuan Pern Tan et al.   NUCLEIC ACIDS RESEARCH

Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms

(2010) Nikolaos G. Sgourakis et al.   JOURNAL OF MOLECULAR BIOLOGY

Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor

(2010) E. Laine et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Homology modeling in drug discovery: current trends and applications

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

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories

(2009) S. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A novel and efficient tool for locating and characterizing protein cavities and binding sites

(2009) Ashutosh Tripathi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The effect of solvents on the conformations of Amyloid β-peptide (1–42) studied by molecular dynamics simulation

(2008) Cao Yang et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins

(2007) Yeturu Kalidas et al.   JOURNAL OF STRUCTURAL BIOLOGY