Molecular Biology International

Review Article

Virtual Interactomics of Proteins from Biochemical Standpoint

Table 1

Some more recent online accessible bioinformatic tools.


Programs	Purpose	Input	Evaluation tools and procedures	Compared structures	Internet accessibility	References

Program tools

3D-BLAST (two methods)	^*Identification of 23 states of the structural alphabet	PDB ACF	^*SASM	^*structural alphabet sequence databases	http://3d-blast.life.nctu.edu.tw/	[41, 42]
3D-BLAST (two methods)	^*Comparison of protein folds using spherical polar Fourier basis functions.	PDB ACF	^*Carbo-like similarity score	^*SPF shape density rep.	http://threedblast.loria.fr/	[41, 42]
DASMIweb	Online integration, analysis and assessment of distributed protein interaction data and predictions (interactomic mining)	some protein identifiers	literature curation, prediction, 3D analysis	records of interactions	http://www.dasmiweb.de	[17]
FFAS03	Server accepts a user supplied protein sequence and automatically generates a profile, which is then compared with several sets of sequence profiles of proteins databases	QS	PPA	DS	http://ffas.godziklab.org/	[36, 37]
KinasePhos 2.0	Prediction of kinase-specific phosphorylation sites based on the site sequences from databases	QS	k-fold + Jackknife cross-validations	phosphorylation sites from Phospho.ELM Swiss-Prot	http://KinasePhos2.mbc.nctu.edu.tw/	[62]
Phos3D	Method of phosphorylation-site prediction based on 3D structural information associated with 530 phys-chem-pr	QS (+3D context)	SVM, spatial amino acid propensities	PDB coordinates	http://phos3d.mpimp-golm.mpg.de/	[63]
SeSAW	Identification of functionally or evolutionarily conserved motifs based on balancing between sequence and structural similarities	^PDB QF, ID; ^PDB QF, ID, IDt	value SeSAW score	conserved domains templates	http://sysimm.ifrec.osaka-u.ac.jp/SeSAW/	[61]

Databases

ADAN	Prediction of protein-protein interactions of different modular protein domains mediated by linear motifs	PDB ACF	PSSM_PI	integrated DaSt	http://adan-embl.ibmc.umh.es/	[64]
CDD (RPS BLAST)	Conserved domain relationships, domain location of frequent binding sites	QS	model MSA derived PSSM	Conserved domains (PSSM)	http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml http://www.ncbi.nlm.nih.gov/BLAST	[65–67]
GWIDD	Docking database; integrated resource for studies of protein-protein interactions on the genome scale	search interface	docking techniques	DaSt	http://gwidd.bioinformatics.ku.edu	[68]
MegaMotifBase (structural database)	3D motif orientation, intermotif distances, solvent accessibility, secondary structure content, hydrogen bonding, residual packaging, familiar/superfamiliar/none motif relationship	motif or sequence pattern	complex evaluation including projection	DS + DaSt	http://caps.ncbs.res.in/MegaMotifbase/index.html	[69]
PTGL	Database for secondary structure-based protein topologies; visualization of topology diagrams and 3D structures	PDB QF	ULN4D_graph theory	DS + DaSt	http://ptgl.uni-frankfurt.de/	[70]
RsiteDB	Database of protein binding pockets which interact with single strand RNA	PDB code, UPS	3D arrangement of phys-chem-pr	3D-CBP	http://bioinfo3d.cs.tau.ac.il/RsiteDB/	[71]

^*Independent alternatives; 3D-CBP: 3D consensus binding patterns important for protein-nucleotide recognition; DS: database sequences; DSA: double sequence alignment; DaSt: database structures; CS: list of compared sequences; ID, IDt: chain or template ID, respectively; MSA: multiple sequence alignment; QS: query sequence(s) (instead of QS, clonal names or gi numbers can be used in majority of given approaches); phys-chem-pr: physicochemical properties; PDB: Protein data bank; PDB QF: PDB-formatted query file; PDB ACF: PDB-derived atom coordinate file; PPA: profile-profile alignment; PSSM: position-specific scoring matrices; PSSM_PI: PSSM for protein-protein interactions calculated by FoldX; rep.: representations; SASM: structural alphabet substitution matrix; SPF: spherical polar Fourier; SVM: support vector machines; ULN4D_graph theory: unique linear notations of four descriptions for protein structures on different abstraction levels based on graph theory; UPS: unbound protein structure.