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

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HADDOCK:  A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

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Improved protein–ligand docking using GOLD

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PatchDock and SymmDock: servers for rigid and symmetric docking

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A Fast Flexible Docking Method using an Incremental Construction Algorithm

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MolDock: A New Technique for High-Accuracy Molecular Docking

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Novel procedure for modeling ligand/receptor induced fit effects.

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A Critical Assessment of Docking Programs and Scoring Functions

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ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

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Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm

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Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine

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A new method for predicting binding affinity in computer-aided drug design

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Further development and validation of empirical scoring functions for structure-based binding affinity prediction

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

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Protein–ligand docking: Current status and future challenges

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Automated docking with grid‐based energy evaluation

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Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem

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PIPER: An FFT‐based protein docking program with pairwise potentials

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Molecular Recognition and Docking Algorithms

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Protein-based virtual screening of chemical databases. 1, evaluation of different docking/scoring combinations.

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Consensus scoring: a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.

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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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Virtual ligand screening: strategies, perspectives and limitations

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A review of protein-small molecule docking methods

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Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance

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

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Evaluation of Docking Performance: Comparative Data on Docking Algorithms

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Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

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Comparative evaluation of eight docking tools for docking and virtual screening accuracy

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Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design

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QXP: Powerful, rapid computer algorithms for structure-based drug design

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ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility

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Gaussian docking functions

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Detailed Analysis of Scoring Functions for Virtual Screening

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Assessing Scoring Functions for Protein−Ligand Interactions

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Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock

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Molecular Docking and High-Throughput Screening for Novel Inhibitors of Protein Tyrosine Phosphatase-1B

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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

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Development and validation of a modular, extensible docking program: DOCK 5

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Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs

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FlexE: efficient molecular docking considering protein structure variations

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Solvated Interaction Energy (SIE) for Scoring Protein−Ligand Binding Affinities. 1. Exploring the Parameter Space

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Comparison of Topological, Shape, and Docking Methods in Virtual Screening

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Modeling water molecules in protein-ligand docking using GOLD.

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Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

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Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

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Water at biomolecular binding interfaces

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