Table 1: Some more recent online accessible bioinformatic tools.

ProgramsPurposeInputEvaluation tools and proceduresCompared structuresInternet accessibilityReferences

Program tools

3D-BLAST (two methods) *Identification of 23 states of the structural alphabetPDB ACF *SASM *structural alphabet sequence databaseshttp://3d-blast.life.nctu.edu.tw/ [41, 42]
*Comparison of protein folds using spherical polar Fourier basis functions. *Carbo-like similarity score *SPF shape density rep.http://threedblast.loria.fr/
DASMIwebOnline integration, analysis and assessment of distributed protein interaction data and predictions (interactomic mining)some protein identifiersliterature curation, prediction, 3D analysisrecords of interactionshttp://www.dasmiweb.de[17]
FFAS03Server accepts a user supplied protein sequence and automatically generates a profile, which is then compared with several sets of sequence profiles of proteins databasesQSPPADShttp://ffas.godziklab.org/[36, 37]
KinasePhos 2.0Prediction of kinase-specific phosphorylation sites based on the site sequences from databasesQSk-fold + Jackknife cross-validationsphosphorylation sites from Phospho.ELM Swiss-Prothttp://KinasePhos2.mbc.nctu.edu.tw/[62]
Phos3DMethod of phosphorylation-site prediction based on 3D structural information associated with 530 phys-chem-prQS (+3D context)SVM, spatial amino acid propensitiesPDB coordinateshttp://phos3d.mpimp-golm.mpg.de/[63]
SeSAWIdentification of functionally or evolutionarily conserved motifs based on balancing between sequence and structural similarities *PDB QF, ID; *PDB QF, ID, IDt value SeSAW scoreconserved domains templateshttp://sysimm.ifrec.osaka-u.ac.jp/SeSAW/[61]

Databases

ADANPrediction of protein-protein interactions of different modular protein domains mediated by linear motifsPDB ACFPSSM_PIintegrated DaSthttp://adan-embl.ibmc.umh.es/[64]
CDD (RPS BLAST)Conserved domain relationships, domain location of frequent binding sitesQSmodel MSA derived PSSMConserved domains (PSSM)http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
http://www.ncbi.nlm.nih.gov/BLAST
[6567]
GWIDDDocking database; integrated resource for studies of protein-protein interactions on the genome scalesearch interfacedocking techniquesDaSthttp://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 relationshipmotif or sequence patterncomplex evaluation including projectionDS + DaSthttp://caps.ncbs.res.in/MegaMotifbase/index.html[69]
PTGLDatabase for secondary structure-based protein topologies; visualization of topology diagrams and 3D structuresPDB QFULN4D_graph theoryDS + DaSthttp://ptgl.uni-frankfurt.de/[70]
RsiteDBDatabase of protein binding pockets which interact with single strand RNAPDB code, UPS3D arrangement of phys-chem-pr3D-CBPhttp://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.