protein descriptors
Protein Sequence Descriptors
The protein descriptors that are available for calculation with the protein sequence descriptors, are described here, with comments and references.
| DESCRIPTOR | EXPLANATION | COMMENTS/REFERENCES |
|---|---|---|
| AA Composition | Sum of Amino acid composition values(McCaldon & Argos) | https://web.expasy.org/protscale/pscale/A.A.composition.html |
| AA Composition Swissprot | Sum of Amino acid composition values based on proteins in SwissProt | https://web.expasy.org/protscale/pscale/A.A.Swiss-Prot.html |
| AA Flexibility Vihinen | Sum of Amino acid flexibility scale values (Vihinen,Torkkila &Rikonen) | https://www.ncbi.nlm.nih.gov/pubmed/8090708 |
| Aggrescan Number of Hotspots | Number of aggregation hotspots, nHS (from Aggrescan) | http://bioinf.uab.es/aap/aap_help.html |
| Alpha Helix Chou Fasman | Sum of alpha helix propensities (Chou & Fasman) | https://web.expasy.org/protscale/pscale/alpha-helixFasman.html |
| Alpha Helix Deleage Roux | Sum of alpha helix propensities (Deleage & Roux) | https://web.expasy.org/protscale/pscale/alpha-helixRoux.html |
| Alpha Helix Levitt | Sum of alpha helix propensities (Levitt) | https://web.expasy.org/protscale/pscale/alpha-helixLevitt.html |
| Antiparallel Beta Strand | Sum of Conformational preference for antiparallel beta strand (Lifson & Sander) | https://web.expasy.org/protscale/pscale/Antiparallelbeta-strand.html |
| Average Flexibility Bhaskaran | Sum of amino acid average flexibility values (Bhaskaran & Ponnusamy) | https://web.expasy.org/protscale/pscale/Averageflexibility.html |
| Avg Area Buried | Sum of Average area buried on transfer from standard state to folded protein (Rose et al.) | https://web.expasy.org/protscale/pscale/Averageburied.html |
| Beta Sheet Chou Fasman | Sum of beta sheet propensities (Chou & Fasman) | https://web.expasy.org/protscale/pscale/beta-sheetFasman.html |
| Beta Sheet Deleage Roux | Sum of beta sheet propensities (Deleage & Roux) | https://web.expasy.org/protscale/pscale/beta-sheetRoux.html |
| Beta Sheet Levitt | Sum of beta sheet propensities (Levitt) | https://web.expasy.org/protscale/pscale/beta-sheetLevitt.html |
| Beta Turn Chou Fasman | Sum of beta turn propensities (Chou & Fasman) | https://web.expasy.org/protscale/pscale/beta-turnFasman.html |
| Beta Turn Deleage Roux | Sum of beta turn propensities (Deleage & Roux) | https://web.expasy.org/protscale/pscale/beta-turnRoux.html |
| Beta Turn Levitt | Sum of beta turn propensities (Levitt) | https://web.expasy.org/protscale/pscale/beta-turnLevitt.html |
| Bulkiness | Sum of amino acid bulkiness values | https://web.expasy.org/protscale/pscale/Bulkiness.html |
| Coil Deleage Roux | Sum of Conformational parameters for coil (Deleage & Roux) | https://web.expasy.org/protscale/pscale/CoilRoux.html |
| Disorder Propensity DisProt | Sum of disorder promotion propensities | https://www.ncbi.nlm.nih.gov/pubmed/17578581 |
| Disorder Propensity FoldUnfold | Sum of disorder promotion propensities (FoldUnFold) | https://www.ncbi.nlm.nih.gov/pubmed/15498936 |
| Disorder Propensity TOP-IDP | Sum of disorder propensity for intrinsic disorder (TOP-IDP scale) | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2676888/ |
| HPLC HFBA Retention | Sum of scale of Retention coefficient in HFBA | https://web.expasy.org/protscale/pscale/HPLCHFBA.html |
| HPLC Retention pH 2.1 | Sum of scale of Retention coefficients in HPLC, pH 2.1 | https://web.expasy.org/protscale/pscale/HPLC2.1.html |
| HPLC Retention pH 7.4 | Sum of scale of Retention coefficients in HPLC, pH 7.4 | https://web.expasy.org/protscale/pscale/HPLC7.4.html |
| HPLC TFA Retention | Sum of scale of retention coefficients in HPLC/TFA | https://web.expasy.org/protscale/pscale/HPLCTFA.html |
| Hydrophobicity Abraham Leo | Sum of hydrophobicity scale values (Abraham & Leo) | https://web.expasy.org/protscale/pscale/Hphob.Leo.html |
| Hydrophobicity Black | Sum of hydrophobicity scale values (Black) | https://web.expasy.org/protscale/pscale/Hphob.Black.html |
| Hydrophobicity Bull Breese | Sum of hydrophobicity scale values (Bull & Breese) | https://web.expasy.org/protscale/pscale/Hphob.Breese.html |
| Hydrophobicity Chothia | Sum of hydrophobicity scale values based on Proportion of residues 95% buried (Chothia) | https://web.expasy.org/protscale/pscale/Hphob.Chothia.html |
| Hydrophobicity Eisenberg | Sum of Normalized consensus hydrophobicity scale values (Eisenberg et al.) | https://web.expasy.org/protscale/pscale/Hphob.Eisenberg.html |
| Hydrophobicity Fauchere | Sum of hydrophobicity scale values (Fauchere) | https://web.expasy.org/protscale/pscale/Hphob.Fauchere.html |
| Hydrophobicity Guy | Sum of Hydrophobicity scale values based on free energy of transfer (kcal/mole) (Guy) | https://web.expasy.org/protscale/pscale/Hphob.Guy.html |
| Hydrophobicity Hopp Woods | Sum of hydrophilicity scale values (Hopp & Woods) | https://web.expasy.org/protscale/pscale/Hphob.Woods.html |
| Hydrophobicity HPLC Parker | Sum of Hydrophilicity scale derived from HPLC peptide retention times (Parker et al.) | https://web.expasy.org/protscale/pscale/Hphob.Parker.html |
| Hydrophobicity HPLC pH 3.4 Cowan | Sum of Hydrophobicity indices at ph 3.4 determined by HPLC (Cowan & Whittaker) | https://web.expasy.org/protscale/pscale/Hphob.pH3.4.html |
| Hydrophobicity HPLC pH 7.5 Cowan | Sum of Hydrophobicity indices at ph 7.5 determined by HPLC (Cowan & Whittaker) | https://web.expasy.org/protscale/pscale/Hphob.pH7.5.html |
| Hydrophobicity HPLC Wilson | Sum of Hydrophobic constants derived from HPLC peptide retention times (Wilson et al.) | https://web.expasy.org/protscale/pscale/Hphob.Wilson.html |
| Hydrophobicity Janin | Sum of hydrophobicity scale dG of transfer from inside to outside of a globular protein (Janin) | https://web.expasy.org/protscale/pscale/Hphob.Janin.html |
| Hydrophobicity Kyte Doolittle | Sum of hydrophobicity scale values (Kyte & Dolittle) | https://web.expasy.org/protscale/pscale/Hphob.Doolittle.html |
| Hydrophobicity Manavalan | Sum of Average surrounding hydrophobicity scale values (Manavalan & Ponnusamy) | https://web.expasy.org/protscale/pscale/Hphob.Manavalan.html |
| Hydrophobicity Miyazawa Jernigan | Sum of hydrophobicity scale values (Miyazawa & Jernigan) | https://web.expasy.org/protscale/pscale/Hphob.Miyazawa.html |
| Hydrophobicity Rao Argos | Sum of membrane buried helix parameters (Rao & Argos) | https://web.expasy.org/protscale/pscale/Hphob.Argos.html |
| Hydrophobicity Rf Mobility | Sum of hydrophobicity scale values based on Mobilities on chromatography paper (Aboderin) | https://web.expasy.org/protscale/pscale/Hphob.mobility.html |
| Hydrophobicity Rose | Sum of hydrophobicity scale values based on Mean fractional exposed area loss (Rose) | https://web.expasy.org/protscale/pscale/Hphob.Rose.html |
| Hydrophobicity Roseman | Sum of hydrophobicity scale values (Roseman) | https://web.expasy.org/protscale/pscale/Hphob.Roseman.html |
| Hydrophobicity Sweet | Sum of Optimized matching hydrophobicity (OMH) scale values (Sweet) | https://web.expasy.org/protscale/pscale/Hphob.Sweet.html |
| Hydrophobicity Tanford | Sum of hydrophobicity scale values (Tanford) | https://web.expasy.org/protscale/pscale/Hphob.Tanford.html |
| Hydrophobicity Welling | Sum of Antigenicity value (X 10) values (Welling) | https://web.expasy.org/protscale/pscale/Hphob.Welling.html |
| Hydrophobicity Wolfenden | Sum of Hydration potential (kcal/mole) at 25 °C scale values (Wolfenden) | https://web.expasy.org/protscale/pscale/Hphob.Wolfenden.html |
| Molecular Weight | Molecular Weight based on a simple amino acid Mol Wt scale | https://web.expasy.org/protscale/pscale/Molecularweight.html |
| Number Of Codons | Sum of # of codons encoding each amino acid in the universal genetic code | https://web.expasy.org/protscale/pscale/Numbercodons.html |
| Parallel Beta Strand | Sum of Conformational preference values for parallel beta strand (Lifson & Sander) | https://web.expasy.org/protscale/pscale/Parallelbeta-strand.html |
| Percentage Accessible Res | Sum of Molar fraction (%) values (of 3220 accessible residues) (Janin) | https://web.expasy.org/protscale/pscale/accessibleresidues.html |
| Percentage Buried Res | Sum of Molar fraction (%) values (of 2001 buried residues) (Janin) | https://web.expasy.org/protscale/pscale/buriedresidues.html |
| Polarity Grantham | Sum of polarity scale values (Grantham) | https://web.expasy.org/protscale/pscale/PolarityGrantham.html |
| Polarity Zimmerman | Sum of polarity scale values (Zimmerman) | https://web.expasy.org/protscale/pscale/PolarityZimmerman.html |
| Ratio Hetero End Side | Sum of Atomic weight ratio of hetero elements in end group to C in side chain | https://web.expasy.org/protscale/pscale/Ratioside.html |
| Recognition Factors | Sum of recognition factors (average of interaction energy with each 20 aa) of each aa (Fraga) | https://web.expasy.org/protscale/pscale/Recognitionfactors.html |
| Refractivity | Sum of refractivity index of each aa (Jones) | https://web.expasy.org/protscale/pscale/Refractivity.html |
| Relative Mutability | Sum of relative mutability values of aa; with Ala=100 (Dayhoff et al.) | https://web.expasy.org/protscale/pscale/Relativemutability.html |
| Total Beta Strand | Sum of Conformational preference for total beta strand (antiparallel+parallel) (Lifson & Sander) | https://web.expasy.org/protscale/pscale/Totalbeta-strand.html |
| Transmembrane Tendency | Sum of transmembrane tendency values (Zhao & London) | https://web.expasy.org/protscale/pscale/Transmembranetendency.html |
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