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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.
Classification: 3.

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.

Solution method:
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.
  1. The contact potential scores the occurrence of any given type of residue pair in 5 possible contact classes (α-helical contact, parallel β-sheet contact, anti-parallel β-sheet contact, side-chain contact, no contact).
  2. The solvation potential scores the occurrence of any residue type in 2 possible enviroments: buried and solvent exposed. Residue environment is assigned by adapting the LCPO algorithm.
  3. Residues present in the reference primary sequence and not present in the model structure contribute to the model score as solvent exposed and as non contacting all other residues.

Restrictions:
Input format file according to the Protein Data Bank standard

Additional comments:
Parameter values used in the scoring function can be found in the file /folder-to-bachscore/BACH/examples/bach_std.par.

Running time:
Roughly one minute to score one hundred structures on a desktop PC, depending on their size.