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Molecules 2017, 22(12), 2230; doi:10.3390/molecules22122230

3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures

GN7 of the Spanish National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)/Instruct Image Processing Center, 28049 Madrid, Spain
Authors to whom correspondence should be addressed.
Received: 31 October 2017 / Revised: 11 December 2017 / Accepted: 13 December 2017 / Published: 15 December 2017
(This article belongs to the Special Issue Computational Analysis for Protein Structure and Interaction)
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Many studies have used position-specific scoring matrices (PSSM) profiles to characterize residues in protein structures and to predict a broad range of protein features. Moreover, PSSM profiles of Protein Data Bank (PDB) entries have been recalculated in many works for different purposes. Although the computational cost of calculating a single PSSM profile is affordable, many statistical studies or machine learning-based methods used thousands of profiles to achieve their goals, thereby leading to a substantial increase of the computational cost. In this work we present a new database compiling PSSM profiles for the proteins of the PDB. Currently, the database contains 333,532 protein chain profiles involving 123,135 different PDB entries. View Full-Text
Keywords: protein structure; protein databases; machine learning; position-specific scoring matrices protein structure; protein databases; machine learning; position-specific scoring matrices

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Sanchez-Garcia, R.; Sorzano, C.O.S.; Carazo, J.M.; Segura, J. 3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures. Molecules 2017, 22, 2230.

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