Advances and Challenges in Protein-Ligand Docking

Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions

(2010) Sheng-You Huang et al.   Journal of Chemical Information and Modeling

Flexible ligand docking using conformational ensembles

(2010) David M. Lorber et al.   PROTEIN SCIENCE

MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening

(2009) Nicolas Sauton et al.   BMC BIOINFORMATICS

Docking and chemoinformatic screens for new ligands and targets

(2009) Peter Kolb et al.   CURRENT OPINION IN BIOTECHNOLOGY

Automated Docking Screens: A Feasibility Study

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

Multiscale Generalized Born Modeling of Ligand Binding Energies for Virtual Database Screening

(2009) Hao-Yang Liu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Flexible ligand docking to multiple receptor conformations: a practical alternative

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

AIScore  Chemically Diverse Empirical Scoring Function Employing Quantum Chemical Binding Energies of Hydrogen-Bonded Complexes

(2008) Stephan Raub et al.   Journal of Chemical Information and Modeling

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

An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA

(2008) Xiaoyu Zhao et al.   Journal of Chemical Information and Modeling

Lead Finder: An Approach To Improve Accuracy of Protein−Ligand Docking, Binding Energy Estimation, and Virtual Screening

(2008) Oleg V. Stroganov et al.   Journal of Chemical Information and Modeling

Investigation of MM-PBSA Rescoring of Docking Poses

(2008) David C. Thompson 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

Assessment of programs for ligand binding affinity prediction

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

Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes

(2008) Max W. Chang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints

(2008) Michal Brylinski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

How to do an evaluation: pitfalls and traps

(2008) Paul C. D. Hawkins et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?

(2008) Johannes Kirchmair et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Recommendations for evaluation of computational methods

(2008) Ajay N. Jain et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

(2008) Pietro Cozzini 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

RosettaLigand Docking with Full Ligand and Receptor Flexibility

(2008) Ian W. Davis et al.   JOURNAL OF MOLECULAR BIOLOGY

SFCscore: Scoring functions for affinity prediction of protein-ligand complexes

(2008) Christoph A. Sotriffer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS