Virtual Interactomics of Proteins from Biochemical Standpoint

Table 3

Examples of protein docking.

Approach/combination	Investigated molecules	Predicted/investigated partners	Evaluation tools and results	Employed internet addresses	References
Protein-ligand
SwissDock	protein	small molecule (ligand)	FullFitness + RMSD	http://www.swissdock.ch	[183]
Glide (version 5.6)	P-glycoprotein	24 P-gp binders + 102 endogenous molecules	Glide XP score + MM-GB/SA rescoring function	http://pubchem.ncbi.nlm.nih.gov/	[184]
VSDocker (AutoGrid4, AutoDock4, etc.)	protein	small molecule (example with 86 775 ligands)	Δ𝐺bind	http://www.bio.nnov.ru/projects/vsdocker2/	[185]
Opal (Autodock tools)	protein	small molecule (ligand)	Δ𝐺bind	http://kryptonite.ucsd.edu/opal2/dashboard?command=serviceList	[186]
FlexX module of SYBYL 7.0 and FMO	neuraminidase (from N1 subtype of influenza virus)	carboxyhexenyl derivatives or analogues	FlexX energy scores	http://www.rcsb.org/pdb; http://grid.ccnu.edu.cn/	[187]
TarFisDock	protein	drugs	interaction energy	http://www.dddc.ac.cn/tarfisdock/	[188]
KinDOCK	ATP binding sites of PK	focused ligand library	theoretical affinity	http://abcis.cbs.cnrs.fr/kindock	[189]
AutoDock + Gold	Cdc25 dual specificity phosphatases	library of sulfonylated aminothiazoles as inhibitors	Δ𝐺bind + overall Gold fitness function	none	[190]
Molsoft module + ACD database	thyroid hormone receptor	250 000 compounds	EQS score	none	[191]
Protein-protein
ZDOCK	protein	flexible/shape complementary protein	combined evaluation using Fast Fourier Transform	http://zlab.umassmed.edu/zdock/; http://www.fftw.org	[192]; [159, 193]
KBDOCK	protein	protein with hetero-binding site	combined knowledge-based approach	http://kbdock.loria.fr/	[194]
RosettaDock	protein	protein	CAPRI CS	http://rosettadock.graylab.jhu.edu	[195]
ClusPro	protein	protein	combined evaluation	http://cluspro.bu.edu/login.php	[196, 197]
Protein-nucleic acid
DARS-RNP; QUASI-RNP	protein	RNA	knowledge-based potentials for scoring protein-RNA models	http://iimcb.genesilico.pl/RNP/	[198]
protein-DNA docking approaches	transcription factor/protein	DNA	RMSD + knowledge based energy	http://pqs.ebi.ac.uk/; http://sparks.informatics.iupui.edu/czhang/ddna2.html	[199]; [200]
Antigen receptors
DS-QM based peptide binding prediction	HLA-DP2	HLA-DP2 interacting potential TCR ligands	CS following from two different DS-QM	none	[201]
SnugDock	antibody	antigen	paratope based structural optimization + CLEP	http://www.rosettacommons.org/	[202]
pDOCK	MHC I and II	potential TCR ligands	RMSD	http://biolinfo.org/mpid-t2	[203]
MHCsim	MHC I and II	potential TCR ligands	molecular dynamic simulation	http://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; Δ𝐺_bind: 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.