Prediction of Protein-Ligand and Protein-Protein Interactions based on Local Surface Similarity
作者： Claudio Garutti
DOI:
关键词: Surface (mathematics) 、 Protein–protein interaction 、 Protein ligand 、 Function (biology) 、 Similarity (network science) 、 Plasma protein binding 、 Machine learning 、 Mathematics 、 Pairwise comparison 、 Artificial intelligence 、 Computational biology 、 Binding site
摘要: The three-dimensional structure of a protein determines its function. This thesis describes suite methods for the problem binding site recognition, based on spin-images representation molecular surface. A procedure cavity detection is coupled with recog- nition similar regions in two proteins, and applied to comparison protein's cavities, all-to-all pairwise set recognition multiple sites one cavity. All presented can be used screen large collections proteins.
参考文章(41)
Lutz P. Ehrlich, Rebecca C. Wade, Protein‐Protein Docking John Wiley & Sons, Inc.. pp. 61- 97 ,(2001) , 10.1002/0471224413.CH2
G. Patrick Brady Jr., Pieter F.W. Stouten, Fast prediction and visualization of protein binding pockets with PASS. Journal of Computer-aided Molecular Design. ,vol. 14, pp. 383- 401 ,(2000) , 10.1023/A:1008124202956
Bentham Science Publisher Bentham Science Publisher, Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Current Protein & Peptide Science. ,vol. 7, pp. 395- 406 ,(2006) , 10.2174/138920306778559386
Andreas Brakoulias, Richard M. Jackson, Towards a structural classification of phosphate binding sites in protein–nucleotide complexes: An automated all‐against‐all structural comparison using geometric matching Proteins. ,vol. 56, pp. 250- 260 ,(2004) , 10.1002/PROT.20123
Peter G. Wolynes, J. Andrew Mccammon, Stephen C. Harvey, Dynamics of proteins and nucleic acids ,(1987)
Gerard J Kleywegt, Recognition of Spatial Motifs in Protein Structures Journal of Molecular Biology. ,vol. 285, pp. 1887- 1897 ,(1999) , 10.1006/JMBI.1998.2393
K. Asish Xavier, Richard C. Willson, Association and dissociation kinetics of anti-hen egg lysozyme monoclonal antibodies HyHEL-5 and HyHEL-10. Biophysical Journal. ,vol. 74, pp. 2036- 2045 ,(1998) , 10.1016/S0006-3495(98)77910-X
B. Lee, F.M. Richards, The interpretation of protein structures: Estimation of static accessibility Journal of Molecular Biology. ,vol. 55, pp. 379- IN4 ,(1971) , 10.1016/0022-2836(71)90324-X
Martin Weisel, Ewgenij Proschak, Gisbert Schneider, PocketPicker: analysis of ligand binding-sites with shape descriptors Chemistry Central Journal. ,vol. 1, pp. 7- 7 ,(2007) , 10.1186/1752-153X-1-7
Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson, Recognition of functional sites in protein structures. Journal of Molecular Biology. ,vol. 339, pp. 607- 633 ,(2004) , 10.1016/J.JMB.2004.04.012