Binding MOAD (Mother Of All Databases)

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BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

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A Critical Assessment of Docking Programs and Scoring Functions

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Design Patterns

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Prediction of Physicochemical Parameters by Atomic Contributions

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Generalized Born Models of Macromolecular Solvation Effects

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The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures

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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

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A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach

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The PDBbind database: methodologies and updates

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Hydrophobic bonding and accessible surface area in proteins

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The maximal affinity of ligands

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PDBsum: summaries and analyses of PDB structures

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Comparative evaluation of 11 scoring functions for molecular docking.

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Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors

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Molecular Recognition and Docking Algorithms

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Unraveling hot spots in binding interfaces: progress and challenges

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Implications of protein flexibility for drug discovery

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A relationship between protein stability and protein function.

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Structure-based maximal affinity model predicts small-molecule druggability

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Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects

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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

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Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis.

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Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps

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PDBsum: a web-based database of summaries and analyses of all PDB structures

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Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities

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The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

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Two-State Allosteric Behavior in a Single-Domain Signaling Protein

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The Biomolecular Interaction Network Database and related tools 2005 update

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Nature of Forces between Large Molecules of Biological Interest*

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Ligand efficiency indices as guideposts for drug discovery

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Druggability Indices for Protein Targets Derived from NMR-Based Screening Data

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Lead discovery using molecular docking

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GATE

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Inhibition of β-Ketoacyl-Acyl Carrier Protein Synthases by Thiolactomycin and Cerulenin

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Accommodating Protein Flexibility in Computational Drug Design,

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The Protein Data Bank: unifying the archive

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A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes

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Fragment-Based Drug Design: How Big Is Too Big?

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

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A model binding site for testing scoring functions in molecular docking.

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Consensus scoring for protein–ligand interactions

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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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Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model

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Docking: Successes and Challenges

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Information extraction from full text scientific articles: Where are the keywords?

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sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank

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Recent Advances in Docking and Scoring

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MMDB: Entrez's 3D-structure database

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Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding

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Exhaustive docking of molecular fragments with electrostatic solvation

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