skip to main content

DOE PAGESDOE PAGES

Title: Genome scale enzyme–metabolite and drug–target interaction predictions using the signature molecular descriptor

Motivation: Identifying protein enzymatic or pharmacological activities are important areas of research in biology and chemistry. Biological and chemical databases are increasingly being populated with linkages between protein sequences and chemical structures. Additionally, there is now sufficient information to apply machine-learning techniques to predict interactions between chemicals and proteins at a genome scale. Current machine-learning techniques use as input either protein sequences and structures or chemical information. We propose here a method to infer protein–chemical interactions using heterogeneous input consisting of both protein sequence and chemical information. Results: Our method relies on expressing proteins and chemicals with a common cheminformatics representation. We demonstrate our approach by predicting whether proteins can catalyze reactions not present in training sets. We also predict whether a given drug can bind a target, in the absence of prior binding information for that drug and target. Lastly, such predictions cannot be made with current machine-learning techniques requiring binding information for individual reactions or individual targets.
Authors:
 [1] ;  [1] ;  [2] ;  [3] ;  [3]
  1. Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Computational Biosciences Dept.
  2. Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Computer Science & Informatics Department
  3. Sandia National Lab. (SNL-CA), Livermore, CA (United States). Biosystems Research
Publication Date:
Report Number(s):
SAND-2007-1648J
Journal ID: ISSN 1367-4803; 526857
Grant/Contract Number:
AC04-94AL85000
Type:
Accepted Manuscript
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Volume: 24; Journal Issue: 2; Journal ID: ISSN 1367-4803
Publisher:
Oxford University Press
Research Org:
Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Sponsoring Org:
USDOE National Nuclear Security Administration (NNSA)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
OSTI Identifier:
1426948

Faulon, Jean-Loup, Misra, Milind, Martin, Shawn, Sale, Ken, and Sapra, Rajat. Genome scale enzyme–metabolite and drug–target interaction predictions using the signature molecular descriptor. United States: N. p., Web. doi:10.1093/bioinformatics/btm580.
Faulon, Jean-Loup, Misra, Milind, Martin, Shawn, Sale, Ken, & Sapra, Rajat. Genome scale enzyme–metabolite and drug–target interaction predictions using the signature molecular descriptor. United States. doi:10.1093/bioinformatics/btm580.
Faulon, Jean-Loup, Misra, Milind, Martin, Shawn, Sale, Ken, and Sapra, Rajat. 2007. "Genome scale enzyme–metabolite and drug–target interaction predictions using the signature molecular descriptor". United States. doi:10.1093/bioinformatics/btm580. https://www.osti.gov/servlets/purl/1426948.
@article{osti_1426948,
title = {Genome scale enzyme–metabolite and drug–target interaction predictions using the signature molecular descriptor},
author = {Faulon, Jean-Loup and Misra, Milind and Martin, Shawn and Sale, Ken and Sapra, Rajat},
abstractNote = {Motivation: Identifying protein enzymatic or pharmacological activities are important areas of research in biology and chemistry. Biological and chemical databases are increasingly being populated with linkages between protein sequences and chemical structures. Additionally, there is now sufficient information to apply machine-learning techniques to predict interactions between chemicals and proteins at a genome scale. Current machine-learning techniques use as input either protein sequences and structures or chemical information. We propose here a method to infer protein–chemical interactions using heterogeneous input consisting of both protein sequence and chemical information. Results: Our method relies on expressing proteins and chemicals with a common cheminformatics representation. We demonstrate our approach by predicting whether proteins can catalyze reactions not present in training sets. We also predict whether a given drug can bind a target, in the absence of prior binding information for that drug and target. Lastly, such predictions cannot be made with current machine-learning techniques requiring binding information for individual reactions or individual targets.},
doi = {10.1093/bioinformatics/btm580},
journal = {Bioinformatics},
number = 2,
volume = 24,
place = {United States},
year = {2007},
month = {11}
}

Works referenced in this record:

Amino acid substitution matrices from protein blocks.
journal, November 1992
  • Henikoff, S.; Henikoff, J. G.
  • Proceedings of the National Academy of Sciences, Vol. 89, Issue 22, p. 10915-10919
  • DOI: 10.1073/pnas.89.22.10915

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997
  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389