The PDBbind database: methodologies and updates

The Protein Data Bank

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Binding MOAD (Mother Of All Databases)

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VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands

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BindingDB: A Web-Accessible Molecular Recognition Database

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An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein−Ligand Complexes

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The Binding Database: data management and interface design

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SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions

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Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 1. Models without Explicit Constrained Water

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JChem: Java Applets and Modules Supporting Chemical Database Handling from Web Browsers

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A knowledge-based scoring function for protein-ligand interactions: Probing the reference state

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Effect of ligand volume correction on PMF scoring

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Predicting binding modes, binding affinities and `hot spots' for protein-ligand complexes using a knowledge-based scoring function

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Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein–ligand complexes

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A knowledge-based scoring function for protein-ligand interactions: Probing the reference state

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Development of KiBank, a database supporting structure-based drug design

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Reviews in Computational Chemistry

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PDBLIG: Classification of Small Molecular Protein Binding in the Protein Data Bank

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Thermodynamic databases for proteins and protein-nucleic acid interactions

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

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ChEMBL: a large-scale bioactivity database for drug discovery

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MoleculeNet: a benchmark for molecular machine learning

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Opportunities and obstacles for deep learning in biology and medicine

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Benchmarking sets for molecular docking.

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Recent advances and applications of deep learning methods in materials science

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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.

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SAbDab: the structural antibody database

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

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Forging the basis for developing protein-ligand interaction scoring functions.

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Recognizing Pitfalls in Virtual Screening: A Critical Review

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Binding MOAD (Mother Of All Databases)

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Computational approaches to therapeutic antibody design: established methods and emerging trends

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Atomic convolutional networks for predicting protein-ligand binding affinity

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Beware of machine learning-based scoring functions-on the danger of developing black boxes.

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Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes

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Modeling of metal interaction geometries for protein–ligand docking

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Robust scoring functions for protein-ligand interactions with quantum chemical charge models.

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Recent advances in predicting protein–protein interactions with the aid of artificial intelligence algorithms

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Artificial intelligence approaches to human-microbiome protein–protein interactions

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A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions.

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Scoring Functions for Protein–Ligand Interactions

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An approach to creating a more realistic working model from a protein data bank entry

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Intrinsic Disorder in the Protein Data Bank

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Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules

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PDB‐BRE : A ligand–protein interaction binding residue extractor based on Protein Data Bank

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Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB)

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