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NameDescriptionReference
RAP:
RAPDF

RAPDF37
RAPDFi37
Residue specific all atom probability discriminatory function Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. Journal of Molecular Biology 275: 893-914, 1998.
IRAP: BTTRGeneralised all atom probability discriminatory function Bernard B, Samudrala R. A generalized knowledge-based discriminatory function for biomolecular interactions. Proteins: Structure, Function, and Bioinformatics 76: 115-128, 2009.
OIRAP: AEFIBTTR with geometric orientation term Cheng G, Samudrala R. A generalised all-atom geometrical knowledge based scoring function for accurate prediction of protein binding ions, affinities and specificities. To be published.
HCFHydrophobic compactness function Samudrala R, Xia Y, Levitt M, Huang ES. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. In Altman R, Dunker K, Hunter L, Klein T, Lauderdale K, eds. Proceedings of the Pacific Symposium on Biocomputing, 505-516, 1999.
MJMiyazawa-Jernigan potential Park B, Huang ES, Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. Journal of Molecular Biology 266: 831-846, 1997.
ShellShell energy Park B, Huang ES, Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. Journal of Molecular Biology 266: 831-846, 1997.
VDW Van Der Waals force (approximated through Lennard-Jones)Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S and Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 4: 187-217, 1983.
Electrostatics Electrostatics energyBrooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S and Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 4: 187-217, 1983.
SolvationSolvation energy Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S and Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 4: 187-217, 1983.
VolumeVolume of all atomsSamudrala R. RAMP, a suite of programs to aid in the modelling of protein structure and function (Version 0.75beta) [Software]. Available from http://software.compbio.org/ramp/ramp.html, 2009.
RGRadius of gyration of all atoms Samudrala R. RAMP, a suite of programs to aid in the modelling of protein structure and function (Version 0.75beta) [Software]. Available from http://software.compbio.org/ramp/ramp.html, 2009.
RMSDCα RMSD Hung L-H, Samudrala R. Accelerated protein structure comparison using TM-score-GPU. Bioinformatics 28(16): 2191-2, 2012.
TM ScoreTM Score Zhang Y, Skolnick J, Scoring function for automated assessment of protein structure template quality. Proteins 57: 702-710, 2004.

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