Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aeqd_v1_0.tar.gz(24108 Kbytes)|
|Manuscript Title: BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures|
|Authors: E. Sarti, S. Zamuner, P. Cossio, A. Laio, F. Seno, A. Trovato|
|Program title: BACHSCORE|
|Catalogue identifier: AEQD_v1_0|
Distribution format: tar.gz
|Journal reference: Comput. Phys. Commun. 184(2013)2862|
|Programming language: C++.|
|Computer: Any computer capable of running an executable produced by a g++ compiler (4.6.3 version).|
|Operating system: Linux, Unix OS-es.|
|RAM: 1 073 741 824 bytes|
|Keywords: Model quality assessment, Protein structure prediction, Scoring function, Solvation energy, Statistical potential, Web server.|
Nature of problem:
Evaluate the quality of a protein structural model, taking into account the possible "a priori" knowledge of a reference primary sequence that may be different from the amino-acid sequence of the model; the native protein structure should be recognized as the best model.
Model quality is assessed through a scoring function defined as a linear combination of two statistical potentials: a pairwise residue-residue contact potential and a single-residue solvation potential. Potential parameters are determined with a probabilistic bayesian analysis on a data set of protein native structures.
Input format file according to the Protein Data Bank standard
Parameter values used in the scoring function can be found in the file /folder-to-bachscore/BACH/examples/bach_std.par.
Roughly one minute to score one hundred structures on a desktop PC, depending on their size.
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