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

ABSTRACT: 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.

SUBMITTER: Sanchez-Garcia R

PROVIDER: S-EPMC6149929 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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

Sanchez-Garcia Ruben R Sorzano Carlos Oscar Sanchez COS Carazo Jose Maria JM Segura Joan J

Molecules (Basel, Switzerland) 20171215 12

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 ...[more]

PMID: 29244774

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