Tackling the challenges posed by target flexibility in drug design

Elastic Potential Grids: Accurate and Efficient Representation of Intermolecular Interactions for Fully Flexible Docking

(2009) Sina Kazemi et al.   ChemMedChem

Managing protein flexibility in docking and its applications

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

Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes

(2009) Manuel Rueda et al.   Journal of Chemical Information and Modeling

Molecular Dynamics and Free Energy Studies on the Wild-Type and Mutated HIV-1 Protease Complexed with Four Approved Drugs: Mechanism of Binding and Drug Resistance

(2009) Stefano Alcaro et al.   Journal of Chemical Information and Modeling

Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model

(2009) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

(2009) Simone Marsili et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Refinement of the primary hydration shell model for molecular dynamics simulations of large proteins

(2009) Mehdi Bagheri Hamaneh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Fragment-based drug discovery

(2009) Wendy A. Warr   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Binding Site Detection and Druggability Index from First Principles

(2009) Jesus Seco et al.   JOURNAL OF MEDICINAL CHEMISTRY

Automated Docking Screens: A Feasibility Study

(2009) John J. Irwin et al.   JOURNAL OF MEDICINAL CHEMISTRY

Docking Flexible Peptide to Flexible Protein by Molecular Dynamics Using Two Implicit-Solvent Models: An Evaluation in Protein Kinase and Phosphatase Systems

(2009) Zunnan Huang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13

(2009) Lorenz C. Blum et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2009) P. T. Lang et al.   RNA

Flexible ligand docking to multiple receptor conformations: a practical alternative

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

Side-chain conformational space analysis (SCSA): A multi conformation-based QSAR approach for modeling and prediction of protein–peptide binding affinities

(2008) Peng Zhou et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling

(2008) P. Arun Prasad et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

An improved method to predict the entropy term with the MM/PBSA approach

(2008) Jacob Kongsted et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

Recent Developments in Fragment-Based Drug Discovery

(2008) Miles Congreve et al.   JOURNAL OF MEDICINAL CHEMISTRY

Determination of Protein–Ligand Binding Modes Using Complexation-Induced Changes in1H NMR Chemical Shift

(2008) Marina Cioffi et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

Combining Docking, Molecular Dynamics and the Linear Interaction Energy Method to Predict Binding Modes and Affinities for Non-nucleoside Inhibitors to HIV-1 Reverse Transcriptase

(2008) Jens Carlsson et al.   JOURNAL OF MEDICINAL CHEMISTRY

Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking

(2008) Giovanni Bottegoni et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure and function of Rubisco

(2008) Inger Andersson et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Flexible protein–flexible ligand docking with disrupted velocity simulated annealing

(2007) Zunnan Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS