Computational close up on protein-protein interactions: how to unravel the invisible using molecular dynamics simulations?

Modulating protein–protein interactions: the potential of peptides

(2015) Laura Nevola et al.   CHEMICAL COMMUNICATIONS

Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking

(2015) Sheng-You Huang   DRUG DISCOVERY TODAY

The impact of molecular dynamics on drug design: applications for the characterization of ligand–macromolecule complexes

(2015) Jérémie Mortier et al.   DRUG DISCOVERY TODAY

Coiled-Coils in Phage Display Screening: Insight into Exceptional Selectivity Provided by Molecular Dynamics

(2015) Jérémie Mortier et al.   Journal of Chemical Information and Modeling

A new scoring function for protein–protein docking that identifies native structures with unprecedented accuracy

(2015) Irina S. Moreira et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Beware of docking!

(2015) Yu-Chian Chen   TRENDS IN PHARMACOLOGICAL SCIENCES

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing toward the Reality

(2014) Michelle R. Arkin et al.   CHEMISTRY & BIOLOGY

Prospective Virtual Screening in a Sparse Data Scenario: Design of Small-Molecule TLR2 Antagonists

(2014) Manuela S. Murgueitio et al.   ChemMedChem

Sampling the equilibrium kinetic network of Trp-cage in explicit solvent

(2014) Weina Du et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase

(2014) Yibing Shan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Investigating the Dynamic Aspects of Drug-Protein Recognition through a Combination of MD and NMR Analyses: Implications for the Development of Protein-Protein Interaction Inhibitors

(2014) Massimiliano Meli et al.   PLoS One

The Interaction of CRM1 and the Nuclear Pore Protein Tpr

(2014) Charles L. Zhao et al.   PLoS One

β- and γ-Amino Acids at α-Helical Interfaces: Toward the Formation of Highly Stable Foldameric Coiled Coils

(2014) Elisabeth K. Nyakatura et al.   ACS Medicinal Chemistry Letters

Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating

(2014) Ramya Gamini et al.   PLoS Computational Biology

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

(2014) Drazen Petrov et al.   PLoS Computational Biology

An Unusual Interstrand H-Bond Stabilizes the Heteroassembly of Helical αβγ-Chimeras with Natural Peptides

(2013) Elisabeth K. Nyakatura et al.   ACS Chemical Biology

Structure and Shape Effects of Molecular Glue on Supramolecular Tubulin Assemblies

(2013) Matteo Garzoni et al.   ACS Nano

Coarse-Graining Methods for Computational Biology

(2013) Marissa G. Saunders et al.   Annual Review of Biophysics

Effects of ATP and Actin-Filament Binding on the Dynamics of the Myosin II S1 Domain

(2013) Joseph L. Baker et al.   BIOPHYSICAL JOURNAL

Probing the Flexibility of Tropomyosin and Its Binding to Filamentous Actin Using Molecular Dynamics Simulations

(2013) Wenjun Zheng et al.   BIOPHYSICAL JOURNAL

Coarse-grain modelling of protein–protein interactions

(2013) Marc Baaden et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Template-based structure modeling of protein–protein interactions

(2013) Andras Szilagyi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein Interface Pharmacophore Mapping Tools for Small Molecule Protein: Protein Interaction Inhibitor Discovery

(2013) Arnout Voet et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Can emerging drug classes improve R&D productivity?

(2013) Christoph Meier et al.   DRUG DISCOVERY TODAY

TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins

(2013) Daria B. Kokh et al.   Journal of Chemical Information and Modeling

Optimizing Protein–Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field

(2013) Dail E. Chapman et al.   Journal of Chemical Theory and Computation

Lead optimization mapper: automating free energy calculations for lead optimization

(2013) Shuai Liu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Self-assembly of chiral tubules

(2013) Shengfeng Cheng et al.   Soft Matter

Small-Molecule Stabilization of Protein-Protein Interactions: An Underestimated Concept in Drug Discovery?

(2012) Philipp Thiel et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

The Future of Peptide-based Drugs

(2012) David J. Craik et al.   Chemical Biology & Drug Design

How SNARE molecules mediate membrane fusion: Recent insights from molecular simulations

(2012) Herre Jelger Risselada et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Drug discovery in pharmaceutical industry: productivity challenges and trends

(2012) Ish Khanna   DRUG DISCOVERY TODAY

Synergistic Applications of MD and NMR for the Study of Biological Systems

(2012) Olivier Fisette et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Perspective: Alchemical free energy calculations for drug discovery

(2012) David L. Mobley et al.   JOURNAL OF CHEMICAL PHYSICS

Structure-Based Design of High-Affinity Macrocyclic Peptidomimetics to Block the Menin-Mixed Lineage Leukemia 1 (MLL1) Protein–Protein Interaction

(2012) Haibin Zhou et al.   JOURNAL OF MEDICINAL CHEMISTRY

Coarse-Grained Modeling of the Self-Association of Therapeutic Monoclonal Antibodies

(2012) Anuj Chaudhri et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics

(2012) Anshuman Dixit et al.   PLoS One

Modeling of Arylamide Helix Mimetics in the p53 Peptide Binding Site of hDM2 Suggests Parallel and Anti-Parallel Conformations Are Both Stable

(2012) Jonathan C. Fuller et al.   PLoS One

Mapping Paratope on Antithrombotic Antibody 6B4 to Epitope on Platelet Glycoprotein Ibalpha via Molecular Dynamic Simulations

(2012) Xiang Fang et al.   PLoS One

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

Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody

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

Near-atomic resolution structural model of the yeast 26S proteasome

(2012) F. Beck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis for Microtubule Binding and Release by Dynein

(2012) W. B. Redwine et al.   SCIENCE

The Structure of Human Tripeptidyl Peptidase II as Determined by a Hybrid Approach

(2012) Anne-Marie Schönegge et al.   STRUCTURE

The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels

(2012) Danielle E. Chandler et al.   PLoS Computational Biology

Molecular dynamics simulations and drug discovery

(2011) Jacob D Durrant et al.   BMC BIOLOGY

An MD2 Hot-Spot-Mimicking Peptide that Suppresses TLR4-Mediated Inflammatory Response in vitro and in vivo

(2011) Liping Liu et al.   CHEMBIOCHEM

Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics

(2011) Bettina G. Keller et al.   CHEMICAL PHYSICS

Three-dimensional modeling of protein interactions and complexes is going ‘omics

(2011) Amelie Stein et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation

(2011) Jim Pfaendtner et al.   JOURNAL OF MOLECULAR BIOLOGY

Transient pockets on XIAP-BIR2: toward the characterization of putative binding sites of small-molecule XIAP inhibitors

(2011) Susanne Eyrisch et al.   JOURNAL OF MOLECULAR MODELING

Detailed Atomistic Analysis of the HIV-1 Protease Interface

(2011) Sérgio Filipe Sousa et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational Reverse-Engineering of a Spider-Venom Derived Peptide Active Against Plasmodium falciparum SUB1

(2011) Giacomo Bastianelli et al.   PLoS One

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

(2011) F. Noe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrophobic Binding Hot Spots of Bcl-xL Protein−Protein Interfaces by Cosolvent Molecular Dynamics Simulation

(2011) Chao-Yie Yang et al.   ACS Medicinal Chemistry Letters

Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex

(2011) Ruhollah Moussavi-Baygi et al.   PLoS Computational Biology

Identification of the first non-peptidic small molecule inhibitor of the c-Abl/14-3-3 protein–protein interactions able to drive sensitive and Imatinib-resistant leukemia cells to apoptosis

(2010) Valentina Corradi et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Design of novel ligands of CDP-methylerythritol kinase by mimicking direct protein-protein and solvent-mediated interactions

(2010) Victor Giménez-Oya et al.   JOURNAL OF MOLECULAR RECOGNITION

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

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

EMDataBank.org: unified data resource for CryoEM

(2010) C. L. Lawson et al.   NUCLEIC ACIDS RESEARCH

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Computational Analysis of Protein Hotspots

(2010) Chao-Yie Yang et al.   ACS Medicinal Chemistry Letters

A β/γ Motif to Mimic α-Helical Turns in Proteins

(2009) Raheleh Rezaei Araghi et al.   CHEMBIOCHEM

Pharmacophore-Based Discovery of Small-Molecule Inhibitors of Protein-Protein Interactions between HIV-1 Integrase and Cellular Cofactor LEDGF/p75

(2009) Laura De Luca et al.   ChemMedChem

Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography

(2009) Leonardo G. Trabuco et al.   METHODS

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach

(2008) Nicholas W. Kelley et al.   JOURNAL OF CHEMICAL PHYSICS

What induces pocket openings on protein surface patches involved in protein–protein interactions?

(2008) Susanne Eyrisch et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE