Role of protein flexibility in the discovery of new drugs

Dimerization of the core domain of the p53 family: A computational study

(2011) Arumugam Madhumalar et al.   CELL CYCLE

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Differential binding of p53 and nutlin to MDM2 and MDMX: Computational studies

(2010) Thomas Leonard Joseph et al.   CELL CYCLE

Toward the Rational Design of p53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant

(2010) Nicolas Basse et al.   CHEMISTRY & BIOLOGY

Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases

(2010) Alexey Aleksandrov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Many Local Motions Cooperate to Produce the Adenylate Kinase Conformational Transition

(2010) Michael D. Daily et al.   JOURNAL OF MOLECULAR BIOLOGY

A Dynamic Model of HIV Integrase Inhibition and Drug Resistance

(2010) Alex L. Perryman et al.   JOURNAL OF MOLECULAR BIOLOGY

Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

(2010) Panagiotis L. Kastritis et al.   JOURNAL OF PROTEOME RESEARCH

Comparison of Entropic Contributions to Binding in a “Hydrophilic” versus “Hydrophobic” Ligand−Protein Interaction

(2010) Neil R. Syme et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

Pharmacological reactivation of mutant p53: from protein structure to the cancer patient

(2010) K G Wiman   ONCOGENE

Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering

(2010) H. S. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

Mining protein dynamics from sets of crystal structures using “consensus structures”

(2010) Gerard J. P. van Westen et al.   PROTEIN SCIENCE

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100

(2009) Shubhra Dastidar et al.   BMC BIOINFORMATICS

Managing protein flexibility in docking and its applications

(2009) Chandrika B-Rao et al.   DRUG DISCOVERY TODAY

Novel mutant-selective EGFR kinase inhibitors against EGFR T790M

(2009) Wenjun Zhou et al.   NATURE

A new screening assay for allosteric inhibitors of cSrc

(2009) Jeffrey R Simard et al.   Nature Chemical Biology

The role of dynamic conformational ensembles in biomolecular recognition

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

NMR spectroscopy brings invisible protein states into focus

(2009) Andrew J Baldwin et al.   Nature Chemical Biology

The rise of fragment-based drug discovery

(2009) Christopher W. Murray et al.   Nature Chemistry

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

(2009) T. Wlodarski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: Application to H3 antagonists

(2009) Brajesh K. Rai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Trapping Moving Targets with Small Molecules

(2009) G. M. Lee et al.   SCIENCE

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

(2009) Olgun Guvench et al.   PLoS Computational Biology

Flexible ligand docking to multiple receptor conformations: a practical alternative

(2008) Maxim Totrov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Multiple Peptide Conformations Give Rise to Similar Binding Affinities: Molecular Simulations of p53-MDM2

(2008) Shubhra Ghosh Dastidar et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

(2008) K.-i. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induced-fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design

(2008) Yechun Xu et al.   PROTEIN SCIENCE

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE

Modeling and Selection of Flexible Proteins for Structure-Based Drug Design: Backbone and Side Chain Movements in p38 MAPK

(2007) Jyothi Subramanian et al.   ChemMedChem