Convolutional neural network scoring and minimization in the D3R 2017 community challenge

Statistical and machine learning approaches to predicting protein–ligand interactions

(2018) Lucy J Colwell   CURRENT OPINION IN STRUCTURAL BIOLOGY

KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

(2018) José Jiménez et al.   Journal of Chemical Information and Modeling

Visualizing convolutional neural network protein-ligand scoring

(2018) Joshua Hochuli et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Protein–Ligand Scoring with Convolutional Neural Networks

(2017) Matthew Ragoza et al.   Journal of Chemical Information and Modeling

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2017) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Lessons Learned over Four Benchmark Exercises from the Community Structure–Activity Resource

(2016) Heather A. Carlson   Journal of Chemical Information and Modeling

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

(2016) Heather A. Carlson et al.   Journal of Chemical Information and Modeling

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

(2016) Symon Gathiaka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Accurate calculation of the absolute free energy of binding for drug molecules

(2016) Matteo Aldeghi et al.   Chemical Science

Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins

(2015) Hossam M Ashtawy et al.   BMC BIOINFORMATICS

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge

(2015) Richard D. Smith et al.   Journal of Chemical Information and Modeling

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

Deep learning

(2015) Yann LeCun et al.   NATURE

Virtual Screening Strategies in Medicinal Chemistry: The State of the Art and Current Challenges

(2014) Rodolpho Braga et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Scoring Functions for Prediction of Protein-Ligand Interactions

(2013) Jui-Chih Wang et al.   CURRENT PHARMACEUTICAL DESIGN

SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein–Ligand Complexes

(2013) David Zilian et al.   Journal of Chemical Information and Modeling

Predicting Ligand Binding Modes from Neural Networks Trained on Protein–Ligand Interaction Fingerprints

(2013) Vladimir Chupakhin et al.   Journal of Chemical Information and Modeling

Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

(2013) David Ryan Koes et al.   Journal of Chemical Information and Modeling

Computational chemistry and drug discovery: a call to action

(2012) Johanna M Jansen et al.   Future Medicinal Chemistry

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

GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function

(2011) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

Pocketome: an encyclopedia of small-molecule binding sites in 4D

(2011) Irina Kufareva et al.   NUCLEIC ACIDS RESEARCH

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

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

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

Improved Ligand-Protein Binding Affinity Predictions Using Multiple Binding Modes

(2010) Eva Stjernschantz et al.   BIOPHYSICAL JOURNAL

NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein−Ligand Complexes

(2010) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions on a Diverse Test Set

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

Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS

(2009) Oliver Korb et al.   Journal of Chemical Information and Modeling

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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