Multipose Binding in Molecular Docking

Structure of a Glycomimetic Ligand in the Carbohydrate Recognition Domain of C-type Lectin DC-SIGN. Structural Requirements for Selectivity and Ligand Design

(2013) Michel Thépaut et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review

(2012) Tiejun Cheng et al.   AAPS Journal

Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery

(2012) Xuan-Yu Meng et al.   Current Computer-Aided Drug Design

SH3 domain ligand binding: What's the consensus and where's the specificity?

(2012) Kalle Saksela et al.   FEBS LETTERS

A Comparative Assessment of Ranking Accuracies of Conventional and Machine-Learning-Based Scoring Functions for Protein-Ligand Binding Affinity Prediction

(2012) Hossam M. Ashtawy et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

High-Resolution Crystal Structure of Spectrin SH3 Domain Fused with a Proline-Rich Peptide

(2012) Liubov V. Gushchina et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further Improvement

(2012) Paulette A. Greenidge et al.   Journal of Chemical Information and Modeling

A fragment-based approach to the SAMPL3 Challenge

(2012) John L. Kulp et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes: methods behind the HYDE scoring function

(2012) Nadine Schneider et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Characterization of the interaction of interleukin-8 with hyaluronan, chondroitin sulfate, dermatan sulfate and their sulfated derivatives by spectroscopy and molecular modeling

(2011) Annelie Pichert et al.   GLYCOBIOLOGY

Global Free Energy Scoring Functions Based on Distance-Dependent Atom-Type Pair Descriptors

(2011) Christian Kramer et al.   Journal of Chemical Information and Modeling

Three Descriptor Model Sets a High Standard for the CSAR-NRC HiQ Benchmark

(2011) Christian Kramer et al.   Journal of Chemical Information and Modeling

CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes

(2011) James B. Dunbar et al.   Journal of Chemical Information and Modeling

Support Vector Regression Scoring of Receptor–Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries

(2011) Liwei Li et al.   Journal of Chemical Information and Modeling

Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets

(2011) Jui-Hua Hsieh et al.   Journal of Chemical Information and Modeling

CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions

(2011) Richard D. Smith et al.   Journal of Chemical Information and Modeling

Solvated Interaction Energy (SIE) for Scoring Protein–Ligand Binding Affinities. 2. Benchmark in the CSAR-2010 Scoring Exercise

(2011) Traian Sulea et al.   Journal of Chemical Information and Modeling

Improving molecular docking through eHiTS’ tunable scoring function

(2011) Orr Ravitz et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The DINGO dataset: a comprehensive set of data for the SAMPL challenge

(2011) Janet Newman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Two Solutions for the Same Problem: Multiple Binding Modes of Pyrrolidine-Based HIV-1 Protease Inhibitors

(2011) Andreas Blum et al.   JOURNAL OF MOLECULAR BIOLOGY

Improved Ligand-Protein Binding Affinity Predictions Using Multiple Binding Modes

(2010) Eva Stjernschantz et al.   BIOPHYSICAL JOURNAL

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Challenges and advances in computational docking: 2009 in review

(2010) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions

(2010) Sheng-You Huang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Comparative Assessment of Scoring Functions on a Diverse Test Set

(2009) Tiejun Cheng et al.   Journal of Chemical Information and Modeling

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Efficient Free Energy Calculations for Compounds with Multiple Stable Conformations Separated by High Energy Barriers

(2009) Jozef Hritz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Assessment of programs for ligand binding affinity prediction

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

Structural Basis of PxxDY Motif Recognition in SH3 Binding

(2008) Olli Aitio et al.   JOURNAL OF MOLECULAR BIOLOGY

The Thermodynamics of Protein–Ligand Interaction and Solvation: Insights for Ligand Design

(2008) Tjelvar S.G. Olsson et al.   JOURNAL OF MOLECULAR BIOLOGY

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

(2007) N Moitessier et al.   BRITISH JOURNAL OF PHARMACOLOGY