Name | Description | Reference |
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: BTTR | Generalised 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: AEFI | BTTR 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. |
HCF | Hydrophobic 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. |
MJ | Miyazawa-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. |
Shell | Shell 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 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. |
Solvation | Solvation 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. |
Volume | Volume 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. |
RG | Radius 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. |
RMSD | Cα RMSD | Hung L-H, Samudrala R. Accelerated protein structure comparison using TM-score-GPU. Bioinformatics 28(16): 2191-2, 2012. |
TM Score | TM Score | Zhang Y, Skolnick J, Scoring function for automated assessment of protein structure template quality. Proteins 57: 702-710, 2004. |