A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction.

By Thomas Rush III, J. A. Grant, L. Mosyak, Anthony Nicholls. 2005

556 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Pharmacology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Evan E. Bolton
2. Stephen H. Bryant
3. Sunghwan Kim
4. Vijay S. Pande
5. Steven M. Kearnes
6. Patrick F. Riley
7. Jürgen Bajorath
8. Kevin McCloskey

In Molecular Biology

1. Sunghwan Kim
2. Evan E. Bolton
3. Stephen H. Bryant
4. Jens Meiler
5. Hanna Eckert
6. Sandeepkumar Kothiwale
7. E. W. Lowe
8. Gregory Sliwoski

In Pharmacology

1. Sunghwan Kim
2. Evan E. Bolton
3. Stephen H. Bryant
4. Jürgen Bajorath
5. Sandeepkumar Kothiwale
6. Jens Meiler
7. E. W. Lowe
8. Vijay S. Pande

Citations in the corpus

• Molecular graph convolutions: moving beyond fingerprints (2016, background): “Rapid overlay of chemical structures (ROCS) aligns pairs of pre-generated conformers and calculates shape and electrostatic (“color”) similarity us-ing Gaussian representations of atoms and color features defined by a simple force field (Rush et al., 2005).”
• PubChem3D: Conformer generation (2011, background): “where VAA and VBB are the self-overlap volume of A and B, respectively, and VAB is the overlap volume between A and B [24-26].”
• PubChem3D: Biologically relevant 3-D similarity (2011, unknown): “PubChem3D uses two 3-D similarity measures: shapeTanimoto (ST) [24,27-30] and color-Tanimoto (CT) [24,27,28].”
• Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis (2012, methodology): “Note that 2-D similarity methods do not always recognize structural similarity between biologically similar molecules that 3-D similarity methods readily do [8,10,11,14,41-44].”
• PubChem3D: Similar conformers (2011, background): “One of these is the shape Tanimoto (ST) for shape similarity [10-12, 16, 17 where V AA and V BB are the respective self-overlap volume and V AB is the overlap volume of conformers A and B. where, for each of the six independent fictitious feature atom types, V AA and V BB are the respective…”
• Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches. (2007, methodology): “ROCS Gaussian shape models Determines volume overlap as a measure of similarity [ 41 ] Fingerprints are considered to be both methods and descriptors.”