DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

A Hybrid Knowledge-Based and Empirical Scoring Function for Protein–Ligand Interaction: SMoG2016

(2017) Théau Debroise et al.   Journal of Chemical Information and Modeling

GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

(2017) Minkyung Baek et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structure Based docking studies towards exploring potential anti-androgen activity of selected phytochemicals against Prostate Cancer

(2017) Anshika N. Singh et al.   Scientific Reports

Performance of machine-learning scoring functions in structure-based virtual screening

(2017) Maciej Wójcikowski et al.   Scientific Reports

Correcting the impact of docking pose generation error on binding affinity prediction

(2016) Hongjian Li et al.   BMC BIOINFORMATICS

SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity

(2016) Yuedong Yang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models

(2016) Lukas Folkman et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure-based discovery of opioid analgesics with reduced side effects

(2016) Aashish Manglik et al.   NATURE

Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power

(2016) Zhe Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Classification of Current Scoring Functions

(2015) Jie Liu et al.   Journal of Chemical Information and Modeling

Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?

(2014) Pedro J. Ballester et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

Beware of Machine Learning-Based Scoring Functions—On the Danger of Developing Black Boxes

(2014) Joffrey Gabel et al.   Journal of Chemical Information and Modeling

Structure Based Design, Synthesis, Pharmacophore Modeling, Virtual Screening, and Molecular Docking Studies for Identification of Novel Cyclophilin D Inhibitors

(2014) Koteswara Rao Valasani et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction

(2014) Huiying Zhao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Pharmacophore-Based Similarity Scoring for DOCK

(2014) Lingling Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

(2014) Sergio Ruiz-Carmona et al.   PLoS Computational Biology

Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics

(2013) Hongtao Zhao et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein–Ligand Interactions

(2013) Guo-Bo Li et al.   Journal of Chemical Information and Modeling

Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets

(2013) Matthias R. Bauer et al.   Journal of Chemical Information and Modeling

GalaxyDock2: Protein-ligand docking using beta-complex and global optimization

(2013) Woong-Hee Shin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation

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

DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes

(2011) Gerd Neudert et al.   Journal of Chemical Information and Modeling

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function

(2010) H. Zhao et al.   BIOINFORMATICS

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

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

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets

(2010) H. Zhao et al.   NUCLEIC ACIDS RESEARCH

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles

(2009) Beisi Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

(2008) Yuedong Yang et al.   PROTEIN SCIENCE

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE