- [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 , in press. (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]