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Binding MOAD, a high-quality protein-ligand database.

Mark L Benson1, Richard D Smith, Nickolay A Khazanov

  • 1Bioinformatics Graduate Program, Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109, Torrey Path LLC, Ann Arbor, MI 48104, USA.

Nucleic Acids Research
|December 7, 2007
PubMed
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Binding MOAD is a growing database of protein-ligand structures, now with enhanced usability and freely available data. It aids researchers in exploring binding affinities and chemical data for drug discovery.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Cheminformatics

Background:

  • Binding MOAD (Mother of All Databases) is a curated repository of protein-ligand crystal structures.
  • The database has experienced significant growth since its inception in 2004, with annual updates.

Purpose of the Study:

  • To present the expanded Binding MOAD database, highlighting its increased size and improved features.
  • To provide researchers with a freely accessible platform for exploring protein-ligand interactions and binding data.

Main Methods:

  • Utilized natural language processing to facilitate database expansion.
  • Integrated advanced visualization tools for examining protein-ligand complexes.
  • Enriched ligand entries with additional chemical data for cheminformatics analysis.

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Main Results:

  • The database now contains 9836 protein-ligand crystal structures, nearly doubling its original size.
  • Enhanced website usability includes a faster, more featured viewer and direct access without logins.
  • Ligands are annotated with biologically relevant information and available binding-affinity data.

Conclusions:

  • Binding MOAD is a valuable, continuously expanding resource for structural biology and drug discovery research.
  • The database's improved accessibility and data richness empower cheminformatics mining and structural analysis.