Table 3: Examples of protein docking.

Approach/combinationInvestigated moleculesPredicted/investigated partnersEvaluation tools and resultsEmployed internet addressesReferences


SwissDockproteinsmall molecule (ligand)FullFitness + RMSD[183]
Glide (version 5.6)P-glycoprotein24 P-gp binders + 102 endogenous moleculesGlide XP score + MM-GB/SA rescoring function[184]
VSDocker (AutoGrid4, AutoDock4, etc.)proteinsmall molecule (example with 86 775 ligands)[185]
Opal (Autodock tools)proteinsmall molecule (ligand)[186]
FlexX module of SYBYL 7.0 and FMOneuraminidase (from N1 subtype of influenza virus)carboxyhexenyl derivatives or analoguesFlexX energy scores
TarFisDockproteindrugsinteraction energy[188]
KinDOCKATP binding sites of PKfocused ligand librarytheoretical affinity[189]
AutoDock + GoldCdc25 dual specificity phosphataseslibrary of sulfonylated aminothiazoles as inhibitors + overall Gold fitness functionnone[190]
Molsoft module + ACD databasethyroid hormone receptor250 000 compoundsEQS scorenone[191]


ZDOCKproteinflexible/shape complementary proteincombined evaluation using Fast Fourier Transform
[159, 193]
KBDOCKproteinprotein with hetero-binding sitecombined knowledge-based approach[194]
RosettaDockproteinproteinCAPRI CS[195]
ClusProproteinproteincombined evaluation[196, 197]

Protein-nucleic acid

proteinRNAknowledge-based potentials for scoring protein-RNA models[198]
protein-DNA docking approachestranscription factor/proteinDNARMSD + knowledge based energy

Antigen receptors

DS-QM based peptide binding predictionHLA-DP2HLA-DP2 interacting potential TCR ligandsCS following from two different DS-QMnone[201]
SnugDockantibodyantigenparatope based structural optimization + CLEP[202]
pDOCKMHC I and IIpotential TCR ligandsRMSD[203]
MHCsimMHC I and IIpotential TCR ligandsmolecular dynamic simulation[204]

ACD: available chemicals directory (database); CAPRI: critical assessment of predicted interactions; CLEP: combined lowest energy prediction; CS: combined scoring; DS-QM: docking score-based quantitative matrices; EQS score: score combining grid energy, electrostatic and entropy terms; FMO: fragment molecular orbitals; HLA-DP: a subset of human MHC II; : free energy of binding; PK: protein kinases; MM-GB/SA molecular mechanics scoring function with generalized Born implicit solvent effects; P-gp: P-glycoprotein; RMSD: root mean square displacement statistics; TCR: T-cell receptor.