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  1. [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]

  2. [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]

  3. [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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