Table 3: Examples of protein docking.

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

Protein-ligand

SwissDockproteinsmall molecule (ligand)FullFitness + RMSDhttp://www.swissdock.ch[183]
Glide (version 5.6)P-glycoprotein24 P-gp binders + 102 endogenous moleculesGlide XP score + MM-GB/SA rescoring functionhttp://pubchem.ncbi.nlm.nih.gov/[184]
VSDocker (AutoGrid4, AutoDock4, etc.)proteinsmall molecule (example with 86 775 ligands) http://www.bio.nnov.ru/projects/vsdocker2/[185]
Opal (Autodock tools)proteinsmall molecule (ligand) http://kryptonite.ucsd.edu/opal2/dashboard?command=serviceList[186]
FlexX module of SYBYL 7.0 and FMOneuraminidase (from N1 subtype of influenza virus)carboxyhexenyl derivatives or analoguesFlexX energy scoreshttp://www.rcsb.org/pdb
http://grid.ccnu.edu.cn/
[187]
TarFisDockproteindrugsinteraction energyhttp://www.dddc.ac.cn/tarfisdock/[188]
KinDOCKATP binding sites of PKfocused ligand librarytheoretical affinityhttp://abcis.cbs.cnrs.fr/kindock[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]

Protein-protein

ZDOCKproteinflexible/shape complementary proteincombined evaluation using Fast Fourier Transformhttp://zlab.umassmed.edu/zdock/
http://www.fftw.org
[192]
[159, 193]
KBDOCKproteinprotein with hetero-binding sitecombined knowledge-based approachhttp://kbdock.loria.fr/[194]
RosettaDockproteinproteinCAPRI CShttp://rosettadock.graylab.jhu.edu[195]
ClusProproteinproteincombined evaluationhttp://cluspro.bu.edu/login.php[196, 197]

Protein-nucleic acid

DARS-RNP
QUASI-RNP
proteinRNAknowledge-based potentials for scoring protein-RNA modelshttp://iimcb.genesilico.pl/RNP/[198]
protein-DNA docking approachestranscription factor/proteinDNARMSD + knowledge based energyhttp://pqs.ebi.ac.uk/
http://sparks.informatics.iupui.edu/czhang/ddna2.html
[199]
[200]

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 + CLEPhttp://www.rosettacommons.org/[202]
pDOCKMHC I and IIpotential TCR ligandsRMSDhttp://biolinfo.org/mpid-t2[203]
MHCsimMHC I and IIpotential TCR ligandsmolecular dynamic simulationhttp://igrid-ext.cryst.bbk.ac.uk/MHCsim/[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.