Softwares

MDockPeP2 - Predicting protein-peptide complex structures by accounting for peptide flexibility and physicochemical environment.
MDock - an automated molecular docking software which can simultaneously docking ligands against multiple protein structures/conformations by using the ensemble docking algorithm
ITScorePro - Statistical mechanics-based energy scoring function for structural model selection in protein structure prediction
ITScorePR - is a statistical mechanics-based energy scoring function for evaluation of the binding tightness of a given protein-RNA structure

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Datasets

ITScore Training set: 786 protein-ligand complex structures for ITScore (download)
ITScore Test sets: The 140 protein-ligand complexes used for validating ITScore (download)
ITScorePP Training set (pdb files): The clean receptor and ligand pdb files of 851 complexes for training ITScore-PP (download)
Protein-RNA docking benchmark: The non-redundant structure dataset for benchmarking protein-RNA computational docking algorithms (link)
Protein-RNA docking decoys: The bound and unbound docking decoy sets for assessment of protein-RNA docking algorithms (link)
SM-TF database: A structural database of small molecule-transcription factor complexes. (link)
PepPro:A Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking. (link)

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Web Servers

MDockPeP: A fully blind docking server for protein-peptide complex structure predictin. (Link)
Accluster: A web server for predicting peptide binding sites on protein surfaces. (Link)