Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches

On the Origin of the Stronger Binding of PIB over Thioflavin T to Protofibrils of the Alzheimer Amyloid-β Peptide: A Molecular Dynamics Study

(2011) Chun Wu et al.   BIOPHYSICAL JOURNAL

Naproxen Interferes with the Assembly of Aβ Oligomers Implicated in Alzheimer's Disease

(2011) Seongwon Kim et al.   BIOPHYSICAL JOURNAL

Calculation of binding free energies of inhibitors to plasmepsin II

(2011) Denise Steiner et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

(2011) Elizabeth J. Denning et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

SwissParam: A fast force field generation tool for small organic molecules

(2011) Vincent Zoete et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Monte Carlo Study of the Formation and Conformational Properties of Dimers of Aβ42 Variants

(2011) Simon Mitternacht et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Basis for Aβ1–42 Toxicity Inhibition by Aβ C-Terminal Fragments: Discrete Molecular Dynamics Study

(2011) B. Urbanc et al.   JOURNAL OF MOLECULAR BIOLOGY

pyDockCG: New Coarse-Grained Potential for Protein–Protein Docking

(2011) Albert Solernou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions

(2011) Ilyas Yildirim et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Rational Design of β-Sheet Ligands Against Aβ42-Induced Toxicity

(2011) Katrin Hochdörffer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How Does a Drug Molecule Find Its Target Binding Site?

(2011) Yibing Shan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure and function of an irreversible agonist-β2 adrenoceptor complex

(2011) Daniel M. Rosenbaum et al.   NATURE

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

PubChem3D: Conformer generation

(2011) Evan E Bolton et al.   Journal of Cheminformatics

Mapping Conformational Ensembles of Aβ Oligomers in Molecular Dynamics Simulations

(2010) Seongwon Kim et al.   BIOPHYSICAL JOURNAL

The Role of Water Molecules in Computational Drug Design

(2010) Stephanie de Beer et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Multiscale investigation of chemical interference in proteins

(2010) Antonios Samiotakis et al.   JOURNAL OF CHEMICAL PHYSICS

Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations

(2010) Sijung Yun et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Nonsteroidal Anti-inflammatory Drug Naproxen Destabilizes Aβ Amyloid Fibrils: A Molecular Dynamics Investigation

(2010) Takako Takeda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model

(2010) Christopher M. Baker et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Transmembrane Structures for Alzheimer’s Aβ1−42Oligomers

(2010) Birgit Strodel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Elucidation of Amyloid β-Protein Oligomerization Mechanisms: Discrete Molecular Dynamics Study

(2010) B. Urbanc et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Building Macromolecular Assemblies by Information-driven Docking

(2010) Ezgi Karaca et al.   MOLECULAR & CELLULAR PROTEOMICS

Protein–protein docking tested in blind predictions: the CAPRI experiment

(2010) Joël Janin   Molecular BioSystems

Frog2: Efficient 3D conformation ensemble generator for small compounds

(2010) M. A. Miteva et al.   NUCLEIC ACIDS RESEARCH

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking

(2010) E. Mashiach et al.   NUCLEIC ACIDS RESEARCH

Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease

(2010) Paulo Ricardo Batista et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Complete Phenotypic Recovery of an Alzheimer's Disease Model by a Quinone-Tryptophan Hybrid Aggregation Inhibitor

(2010) Roni Scherzer-Attali et al.   PLoS One

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

(2010) C. F. Abrams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Side-chain rotamer transitions at protein-protein interfaces

(2010) Mainak Guharoy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques

(2009) Ryan Brenke et al.   BIOINFORMATICS

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

GROMOS96 43a1 performance in predicting oligosaccharide conformational ensembles within glycoproteins

(2009) C.L. Fernandes et al.   CARBOHYDRATE RESEARCH

Structure-Based Virtual Ligand Screening: Recent Success Stories

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

Molecular Recognition and Drug-Lead Identification: What Can Molecular Simulations Tell Us?

(2009) G. Morra et al.   CURRENT MEDICINAL CHEMISTRY

Biophysical techniques for ligand screening and drug design

(2009) Jean-Paul Renaud et al.   CURRENT OPINION IN PHARMACOLOGY

Computational evaluation of protein–small molecule binding

(2009) Olgun Guvench et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Linking folding and binding

(2009) Peter E Wright et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Prospective Ligand- and Target-Based 3D QSAR: State of the Art 2008

(2009) Robert Clark   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Improved Binding of Raf to Ras·GDP Is Correlated with Biological Activity

(2009) Christina Kiel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Docking, virtual high throughput screening and in silico fragment-based drug design

(2009) Vincent Zoete et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

LigMatch: A Multiple Structure-Based Ligand Matching Method for 3D Virtual Screening

(2009) Sarah L. Kinnings et al.   Journal of Chemical Information and Modeling

Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy

(2009) Jason B. Cross et al.   Journal of Chemical Information and Modeling

Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange

(2009) Yuguang Mu   JOURNAL OF CHEMICAL PHYSICS

Coarse-Grained MD Simulations and Protein−Protein Interactions: The Cohesin−Dockerin System

(2009) Benjamin A. Hall et al.   Journal of Chemical Theory and Computation

Charge Recombination Kinetics and Protein Dynamics in Wild Type and Carotenoid-less Bacterial Reaction Centers: Studies in Trehalose Glasses

(2009) Francesco Francia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structures and Thermodynamics of Alzheimer’s Amyloid-β Aβ(16−35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length Aβ Fibrillation

(2009) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring Complex Protein−Ligand Recognition Mechanisms with Coarse Metadynamics

(2009) Matteo Masetti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Importance of Ligand Reorganization Free Energy in Protein−Ligand Binding-Affinity Prediction

(2009) Chao-Yie Yang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of dynamic conformational ensembles in biomolecular recognition

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

Amyloid-β protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease

(2009) Summer L. Bernstein et al.   Nature Chemistry

PEP-FOLD: an online resource for de novo peptide structure prediction

(2009) J. Maupetit et al.   NUCLEIC ACIDS RESEARCH

Simultaneous prediction of protein folding and docking at high resolution

(2009) Rhiju Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative binding energy analysis for binding affinity and target selectivity prediction

(2009) Stefan Henrich et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

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

(2009) David L. Mobley et al.   STRUCTURE

Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments

(2009) Roberto Mosca et al.   PLoS Computational Biology

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

(2009) Noriaki Okimoto et al.   PLoS Computational Biology

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening

(2009) Nobuyoshi Nagamine et al.   PLoS Computational Biology

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

Role of the Region 23-28 in Aβ Fibril Formation: Insights from Simulations of the Monomers and Dimers of Alzheimers Peptides Aβ40 and Aβ42

(2008) Adrien Melquiond et al.   Current Alzheimer Research

Flexible ligand docking to multiple receptor conformations: a practical alternative

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

Probing protein aggregation using discrete molecular dynamics

(2008) Shantanu Sharma   Frontiers in Bioscience-Landmark

MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization

(2008) Cristiano R. W. Guimarães et al.   Journal of Chemical Information and Modeling

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

(2008) Shuangye Yin et al.   Journal of Chemical Information and Modeling

Ranking Targets in Structure-Based Virtual Screening of Three-Dimensional Protein Libraries: Methods and Problems

(2008) Esther Kellenberger et al.   Journal of Chemical Information and Modeling

Assessment of programs for ligand binding affinity prediction

(2008) Ryangguk Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Computational Redesign of the SHV-1 β-Lactamase/β-Lactamase Inhibitor Protein Interface

(2008) Kimberly A. Reynolds et al.   JOURNAL OF MOLECULAR BIOLOGY

Identification of Protein Interaction Partners and Protein–Protein Interaction Sites

(2008) Sophie Sacquin-Mora et al.   JOURNAL OF MOLECULAR BIOLOGY

Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent

(2008) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations

(2008) Anna Berteotti et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS

The RosettaDock server for local protein-protein docking

(2008) S. Lyskov et al.   NUCLEIC ACIDS RESEARCH

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

(2008) S. E. Dobbins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

C-terminal peptides coassemble into A 42 oligomers and protect neurons against A 42-induced neurotoxicity

(2008) E. A. Fradinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein-protein docking by simulating the process of association subject to biochemical constraints

(2008) Domantas Motiejunas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 3.0

(2008) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Targeting the early steps of Aβ16-22 protofibril disassembly by N-methylated inhibitors: A numerical study

(2008) Yassmine Chebaro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Incorporating high-throughput proteomics experiments into structural biology pipelines: Identification of the low-hanging fruits

(2008) Roland A. Pache et al.   PROTEOMICS

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

(2008) O. F. Lange et al.   SCIENCE

Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

(2008) Feng Ding et al.   STRUCTURE

Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling

(2008) Benoit Adam et al.   BMC STRUCTURAL BIOLOGY

Electrostatics in protein-protein docking

(2002) Alexander Heifetz et al.   PROTEIN SCIENCE