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. 2018 Jul 31;20(5):1878–1912. doi: 10.1093/bib/bby061

Table 5.

Libraries and toolkits for protein analysis (including VS)

Tools and libraries Basic properties and included descriptorsa Operating systems Programming languages
PROFEAT [95], ProPy [135], PyDPI [136] AAC, DC, TC (ProPy and PyDPI), autocorrelation, CTD, CTriad (only PyDPI), SOCN, QSO, Pse-AAC, Am-Pse-AAC, topological descriptors (only PROFEAT), total amino acid properties (only PROFEAT) Microsoft Windows, Linux PROFEAT:

  • Web server

  • ProPy: Python

  • PyDPI: Python
protr/ProtrWebb [137], Rcpi [138] AAC, DC, TC, autocorrelation, CTD, CTriad, SOCN, QSO, Pse-AAC, Am-Pse-AAC, scales-based descriptors derived by PCA, factor analysis, and multidimensional scaling, BLOSUM/PAM matrix derived descriptors, PSSM profiles, similarity measures based on sequence alignment and GO annotation semantic similarity Microsoft Windows, Linux, MacOSX protr/ProtrWeb:

  • Web server, R
camb [139] AAC, DC, TC, autocorrelation, CTD, CTriad, SOCN, QSO, Pse-AAC, Am-Pse-AAC, Z-scales, T-scales, ST-scales, VHSE, MSWHIM, FASGAI, ProtFP8, BLOSUM62 Linux, Mac OS C++, Java, Python, R
ProFET [140] Various features based on biophysical quantitative properties, letter-based features, local potential features, information-based statistics, AA scale-based features, and transformed CTD features Linux Python
BLAST [141], ClustalWc [142] Heuristic pairwise sequence alignments/database search (BLAST), multiple sequence alignments (ClustalW) Microsoft Windows, Linux, MacOSX Web server, C, C++
DALI [143], MultiProt [144], TM-align [145], RCSB PDB Comparison Tool [146] Protein global structure alignments

  • MultiProt:Linux,

  • TM-align: Linux

 All: Web server,TM-align:Fortran, C++
SiteEngine [147], APoc [148], eMatchSite [149], G-LosA [150] Protein local structure alignmentsd Linux

  • SiteEngine/eMatchSite: Web server

  • G-LosA/eMatchSite:

  • C++
POSSUM [151] PSSM profile-based feature descriptors Microsoft Windows, Linux, MacOSX Web server, Perl, Python
GOSemSim [152] Gene Ontology annotation semantic similarity Microsoft Windows, Linux, MacOSX R
FragHMMent [153] Prediction of residue-residue contacts Linux Java
PSIPRED [154] Secondary structure prediction Linux Web server, C
Naccess [155], POPS [156] Solvent accessible surface area Naccess: Linux, POPS: Microsoft Windows, Linux, MacOSX Naccess: Fortran, POPS: Java
PocketPicker [157] Prediction of protein binding pockets Linux PyMol plugin
SCREENc [158], trj_cavity [159] Identification of protein cavities trj_cavity: Linux SCREEN: Web server, trj_cavity: C++
a

Descriptor names are abbreviated according to information in Section 2.B Target Protein Descriptors.

b

ProtrWeb only provides AAC, DC, TC, Autocorrelation, CTD, CTriad, SOCN, QSO, Pse-AAC and Am-Pse-AAC descriptors.

c

ClustalW has been retired and replaced with Clustal Omega. The original SCREEN tool is also replaced with SCREEN2.

d

These tools can also be included in ‘prediction of protein binding pockets’ part, which are mainly used for this purpose.