LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters

No abstract is available for this paper.

• Publication year

  2005

• Venue

  Journal of Chemical Information and Modeling

• Publication date

  Unknown publication date

• Fields of study

  Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1021/ci049885ePMID 15667141
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  1996cited by this paper
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  1996cited by this paper
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  1996cited by this paper
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  1995cited by this paper
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  1995cited by this paper
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  1995cited by this paper
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  1994cited by this paper
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