Research Article

Binding MOAD (Mother Of All Databases)

  1. Liegi Hu1,
  2. Mark L. Benson2,
  3. Richard D. Smith3,
  4. Michael G. Lerner3,
  5. Heather A. Carlson1,2,3,*

Article first published online: 21 JUN 2005

DOI: 10.1002/prot.20512

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 60, Issue 3, pages 333–340, 15 August 2005

Additional Information

How to Cite

Hu, L., Benson, M. L., Smith, R. D., Lerner, M. G. and Carlson, H. A. (2005), Binding MOAD (Mother Of All Databases). Proteins: Structure, Function, and Bioinformatics, 60: 333–340. doi: 10.1002/prot.20512

Author Information

  1. 1

    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan

  2. 2

    Bioinformatics Program, University of Michigan, Ann Arbor, Michigan

  3. 3

    Biophysics Research Division, University of Michigan, Ann Arbor, Michigan

*University of Michigan, College of Pharmacy, 428 Church St., Ann Arbor, MI 48109-1065

Publication History

  1. Issue published online: 12 JUL 2005
  2. Article first published online: 21 JUN 2005
  3. Manuscript Received: 16 SEP 2005
  4. Manuscript Accepted: 30 JAN 2005

Funded by

  • Beckman Young Investigator Award Program (HAC)
  • National Institute of General Medical Sciences. Grant Number: HAC GM065372
  • University of Michigan's Molecular Biophysics Training Program. Grant Number: NIGMS grant GM008270

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Keywords:

  • protein–ligand complex;
  • binding affinity;
  • redundancy;
  • PDB;
  • scoring function;
  • inverse docking;
  • structure-based drug discovery;
  • molecular recognition

Abstract

Binding MOAD (Mother of All Databases) is the largest collection of high-quality, protein–ligand complexes available from the Protein Data Bank. At this time, Binding MOAD contains 5331 protein–ligand complexes comprised of 1780 unique protein families and 2630 unique ligands. We have searched the crystallography papers for all 5000+ structures and compiled binding data for 1375 (26%) of the protein–ligand complexes. The binding-affinity data ranges 13 orders of magnitude. This is the largest collection of binding data reported to date in the literature. We have also addressed the issue of redundancy in the data. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 “best” complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This significant collection of protein–ligand complexes will be very useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques. The dataset can be accessed at http://www.BindingMOAD.org. Proteins 2005. © 2005 Wiley-Liss, Inc.

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