Protein Surface Representation and Comparison: New Approaches in Structural Proteomics

5.

[1]  Jie Liang,et al.  Inferring functional relationships of proteins from local sequence and spatial surface patterns. , 2003, Journal of molecular biology.

[2]  D Fischer,et al.  Molecular surface representations by sparse critical points , 1994, Proteins.

[3]  Andrea J. van Doorn,et al.  Surface shape and curvature scales , 1992, Image Vis. Comput..

[4]  Alessandra Lumini,et al.  Clustering techniques for protein surfaces , 2006, Pattern Recognit..

[5]  Tsuhan Chen,et al.  Efficient feature extraction for 2D/3D objects in mesh representation , 2001, Proceedings 2001 International Conference on Image Processing (Cat. No.01CH37205).

[6]  Christian Hofbauer,et al.  SURFCOMP: A Novel Graph-Based Approach to Molecular Surface Comparison , 2004, J. Chem. Inf. Model..

[7]  Andrew E. Johnson,et al.  Using Spin Images for Efficient Object Recognition in Cluttered 3D Scenes , 1999, IEEE Trans. Pattern Anal. Mach. Intell..

[8]  Yang Zhang,et al.  Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment , 2004, Bioinform..

[9]  Bernard Chazelle,et al.  Shape distributions , 2002, TOGS.

[10]  J. Thornton,et al.  Shape variation in protein binding pockets and their ligands. , 2007, Journal of molecular biology.

[11]  José María Carazo,et al.  Spin Images and Neural Networks for Efficient Content-Based Retrieval in 3D Object Databases , 2002, CIVR.

[12]  A Godzik,et al.  Surface map comparison: studying function diversity of homologous proteins. , 2001, Journal of molecular biology.

[13]  Ruth Nussinov,et al.  Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.

[14]  Mark Gerstein,et al.  A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites , 1992 .

[15]  Thomas A. Funkhouser,et al.  Partial matching of 3D shapes with priority-driven search , 2006, SGP '06.

[16]  M. L. Connolly Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[17]  R. Nussinov,et al.  A geometry-based suite of molecular docking processes. , 1995, Journal of molecular biology.

[18]  Andrew J. Bulpitt,et al.  AI-based Algorithms for Protein Surface Comparisons , 2002, Comput. Chem..

[19]  B. Masek,et al.  Molecular skins: A new concept for quantitative shape matching of a protein with its small molecule mimics , 1993, Proteins.

[20]  P E Bourne,et al.  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.

[21]  Michael G. Strintzis,et al.  3D Content-Based Search Based on 3D Krawtchouk Moments , 2006, Third International Symposium on 3D Data Processing, Visualization, and Transmission (3DPVT'06).

[22]  Szymon Rusinkiewicz,et al.  Rotation Invariant Spherical Harmonic Representation of 3D Shape Descriptors , 2003, Symposium on Geometry Processing.

[23]  M. L. Connolly Shape complementarity at the hemoglobin alpha 1 beta 1 subunit interface. , 1986, Biopolymers.

[24]  Marcin Novotni,et al.  3D zernike descriptors for content based shape retrieval , 2003, SM '03.

[25]  Peter Willett,et al.  Comparison of protein surfaces using a genetic algorithm , 1997, J. Comput. Aided Mol. Des..

[26]  Indriyati Atmosukarto,et al.  3D model retrieval with morphing-based geometric and topological feature maps , 2003, 2003 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2003. Proceedings..

[27]  Bin Li,et al.  Fast protein tertiary structure retrieval based on global surface shape similarity , 2008, Proteins.

[28]  Michael Elad,et al.  Directed Search In A 3D Objects Database Using SVM , 2000 .

[29]  Gabriele Ausiello,et al.  Functional annotation by identification of local surface similarities: a novel tool for structural genomics , 2005, BMC Bioinformatics.

[30]  Remco C. Veltkamp,et al.  A Survey of Content Based 3D Shape Retrieval Methods , 2004, SMI.

[31]  Reinhard Klein,et al.  Shape retrieval using 3D Zernike descriptors , 2004, Comput. Aided Des..

[32]  Ron Meir,et al.  Signatures of 3D Models for Retrieval , 2002 .

[33]  K. Kinoshita,et al.  Identification of protein functions from a molecular surface database, eF-site , 2004, Journal of Structural and Functional Genomics.

[34]  B. Li,et al.  Rapid comparison of properties on protein surface , 2008, Proteins.

[35]  R. Nussinov,et al.  Molecular shape comparisons in searches for active sites and functional similarity. , 1998, Protein engineering.

[36]  Mary Ellen Bock,et al.  Discovery of Similar Regions on Protein Surfaces , 2007, J. Comput. Biol..

[37]  Mohammed J. Zaki,et al.  Context shapes: Efficient complementary shape matching for protein–protein docking , 2008, Proteins.

[38]  D. Ritchie,et al.  Protein docking using spherical polar Fourier correlations , 2000, Proteins.

[39]  Xiong Wang /spl alpha/-surface and its application to mining protein data , 2001, Proceedings 2001 IEEE International Conference on Data Mining.

[40]  Ming Ouhyoung,et al.  On Visual Similarity Based 3D Model Retrieval , 2003, Comput. Graph. Forum.

[41]  Lora Mak,et al.  An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison. , 2008, Journal of molecular graphics & modelling.

[42]  Nikolaos Canterakis,et al.  3D Zernike Moments and Zernike Affine Invariants for 3D Image Analysis and Recognition , 1999 .

[43]  Masayuki Nakajima,et al.  Spherical Wavelet Descriptors for Content-based 3D Model Retrieval , 2006, IEEE International Conference on Shape Modeling and Applications 2006 (SMI'06).