Protinfo Score - documentation

Submission tips
Results
Scoring functions

Submission tips:

You may submit a single PDB file, or multiple PDB files archived in .tar.gz/.tgz format.
Each PDB file should only contain one chain and one model. Only the first chain will be scored if multiple are present.
You may also submit a correct conformation file in .pdb format, to which the protein files will be compared through Ca RMSD and/or TM score.
Sample input is available. Click here to download the accompanying correct conformation file.

Results:

Upon submission, you will receive a link that you can use to access your results after the computation has finished. Please bookmark this link to return to at a later time. Your submission status will also be available at this link.
This link to the results is NOT guaranteed to last. Please save all results.
Any errors encountered in the computation will be included in the results.
Z-scores are calculated from distributions of decoy and solved structures. They are measures of confidence of the scores, not of the proteins themselves.
The lower the score, the more native-like a protein structure is. The only exception is the TM score, which varies from 0 to 1, with 1 indicating a near perfect match to the correct conformation.
Sample results are available.

Scoring functions:

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.

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