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| References |
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- [Real-time structure search and structure classification for AlphaFold protein models]
Aderinwale Tunde, Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh, Yuki Kagaya, and Daisuke Kihara. Real-time structure search and structure classification for AlphaFold protein models. Communications Biology 5: 316, 1-12 (2022).
[Pubmed][PDF]
- [If 3D-surfer is used for publication, please
cite]
David La, Juan Esquivel-Rodriguez,
Vishwesh Venkatraman, Bin Li, Lee Sael, Steven Ueng,
Steven Ahrendt, and Daisuke Kihara. 3D-SURFER:
software for high throughput protein surface
comparison and analysis. Bioinformatics 25:
2843-2844(2009). [Pubmed][PDF]
- [Applcation of the 3D Zernike descriptors for
global protein shape comparison]
Lee Sael, Bin
Li, David La, Yi Fang, Karthik Ramani, Raif Rustamov
and Daisuke Kihara. Fast protein tertiary structure
retrieval based on global surface shape similarity. Proteins:
Structure, Function, and Bioinformatics 72:1259-1273(2008).[Pubmed][PDF]
- [Visgrid algorithm for pocket/protrusion/flat
region detection in protein surface]
Bin Li,
Srinivasan Turuvekere, Manish Agrawal, David La,
Karthik Ramani and Daisuke Kihara. Characterization
of local geometry of protein surfaces with the
Visibility Criterion. Proteins: Structure,
Function, and Bioinformatics 71: 670-683(2008).[Pubmed][PDF]
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