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Open AccessTechnical Note

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