Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space

[1]  David B. Dunson,et al.  Probabilistic topic models , 2011, KDD '11 Tutorials.

[2]  Margarita Osadchy,et al.  Maps of protein structure space reveal a fundamental relationship between protein structure and function , 2011, Proceedings of the National Academy of Sciences.

[3]  Ashish V. Tendulkar,et al.  Multi-view methods for protein structure comparison using latent dirichlet allocation , 2011, Bioinform..

[4]  Hwee Kuan Lee,et al.  Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity , 2010, BMC Bioinformatics.

[5]  Inbal Budowski-Tal,et al.  FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately , 2010, Proceedings of the National Academy of Sciences.

[6]  Ian H. Witten,et al.  The WEKA data mining software: an update , 2009, SKDD.

[7]  Mohammed J. Zaki,et al.  FlexSnap: Flexible Non-sequential Protein Structure Alignment , 2009, WABI.

[8]  Daniel Barbará,et al.  Topic Significance Ranking of LDA Generative Models , 2009, ECML/PKDD.

[9]  Gregory W. Corder,et al.  Nonparametric Statistics for Non-Statisticians: A Step-by-Step Approach , 2009 .

[10]  S. Brenner,et al.  Expectations from structural genomics , 2008, Protein science : a publication of the Protein Society.

[11]  W. Taylor.  Protein structure comparison using iterated double dynamic programming , 2008, Protein science : a publication of the Protein Society.

[12]  Svetlana Kirillova,et al.  Progress in the PRIDE technique for rapidly comparing protein three-dimensional structures , 2008, BMC Research Notes.

[13]  David A. Lee,et al.  Predicting protein function from sequence and structure , 2007, Nature Reviews Molecular Cell Biology.

[14]  A. M. Lisewski,et al.  Rapid detection of similarity in protein structure and function through contact metric distances , 2006, Nucleic acids research.

[15]  Leo S. D. Caves,et al.  Bio3d: An R Package , 2022 .

[16]  Chih-Chieh Chen,et al.  (PS)2: protein structure prediction server , 2006, Nucleic Acids Res..

[17]  Joël Pothier,et al.  YAKUSA: A fast structural database scanning method , 2005, Proteins.

[18]  Russell L. Marsden,et al.  Progress of structural genomics initiatives: an analysis of solved target structures. , 2005, Journal of molecular biology.

[19]  J. Skolnick,et al.  TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.

[20]  Sung-Hou Kim,et al.  Global mapping of the protein structure space and application in structure-based inference of protein function. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Rachel Kolodny,et al.  Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. , 2005, Journal of molecular biology.

[22]  Kian-Lee Tan,et al.  Rapid 3D protein structure database searching using information retrieval techniques , 2004, Bioinform..

[23]  W. Pearson,et al.  Sensitivity and selectivity in protein structure comparison , 2004, Protein science : a publication of the Protein Society.

[24]  Adam Godzik,et al.  Flexible structure alignment by chaining aligned fragment pairs allowing twists , 2003, ECCB.

[25]  Adam Zemla,et al.  LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..

[26]  Robert B Russell,et al.  A model for statistical significance of local similarities in structure. , 2003, Journal of molecular biology.

[27]  P. Røgen,et al.  Automatic classification of protein structure by using Gauss integrals , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[28]  M. Levitt,et al.  Small libraries of protein fragments model native protein structures accurately. , 2002, Journal of molecular biology.

[29]  S. Pongor,et al.  Protein fold similarity estimated by a probabilistic approach based on Cα-Cα distance comparison , 2002 .

[30]  P. Koehl,et al.  Protein structure similarities. , 2001, Current opinion in structural biology.

[31]  Andrew J. Martin,et al.  The ups and downs of protein topology; rapid comparison of protein structure. , 2000, Protein engineering.

[32]  David Haussler,et al.  Using the Fisher Kernel Method to Detect Remote Protein Homologies , 1999, ISMB.

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

[34]  M. Levitt,et al.  A unified statistical framework for sequence comparison and structure comparison. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[36]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[37]  R. Durbin,et al.  Pfam: A comprehensive database of protein domain families based on seed alignments , 1997, Proteins.

[38]  A. Godzik.  The structural alignment between two proteins: Is there a unique answer? , 1996, Protein science : a publication of the Protein Society.

[39]  G. Kleywegt.  Use of non-crystallographic symmetry in protein structure refinement. , 1996, Acta crystallographica. Section D, Biological crystallography.

[40]  J F Gibrat,et al.  Surprising similarities in structure comparison. , 1996, Current opinion in structural biology.

[41]  Michael Gribskov,et al.  Use of Receiver Operating Characteristic (ROC) Analysis to Evaluate Sequence Matching , 1996, Comput. Chem..

[42]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[43]  S. Bryant,et al.  Threading a database of protein cores , 1995, Proteins.

[44]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[45]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[46]  M. Levitt,et al.  Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core , 1993, Current Biology.

[47]  W R Taylor,et al.  Protein structure alignment. , 1989, Journal of molecular biology.

[48]  W R Taylor,et al.  A holistic approach to protein structure alignment. , 1989, Protein engineering.

[49]  A. D. McLachlan,et al.  A mathematical procedure for superimposing atomic coordinates of proteins , 1972 .

[50]  M. Perutz,et al.  Structure of Hæmoglobin: A Three-Dimensional Fourier Synthesis at 5.5-Å. Resolution, Obtained by X-Ray Analysis , 1960, Nature.

[51]  Rachel Kolodny,et al.  Using Protein Fragments for Searching atabases and Data-Mining Protein D , 2013 .

[52]  Emanuele Della Valle,et al.  An Introduction to Information Retrieval , 2013 .

[53]  Mohammed J. Zaki,et al.  ResearchFlexible Non-sequential Protein Structure Alignment , 2010 .

[54]  Gregor Heinrich.  Parameter estimation for text analysis , 2009 .

[55]  Michael I. Jordan,et al.  Latent Dirichlet Allocation , 2009 .

[56]  Oliviero Carugo,et al.  Rapid Methods for Comparing Protein Structures and Scanning Structure Databases , 2006 .

[57]  Amos Bairoch,et al.  Recent improvements to the PROSITE database , 2004, Nucleic Acids Res..

[58]  James E. Bray,et al.  The CATH database: an extended protein family resource for structural and functional genomics , 2003, Nucleic Acids Res..

[59]  Li Liao,et al.  Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships , 2003, J. Comput. Biol..

[60]  Amos Bairoch,et al.  The PROSITE database, its status in 2002 , 2002, Nucleic Acids Res..

[61]  Vladimir N. Vapnik,et al.  The Nature of Statistical Learning Theory , 2000, Statistics for Engineering and Information Science.

[62]  S. Eddy.  Profile hidden Markov models , 1998, Bioinform..

[63]  Chris Sander,et al.  Touring protein fold space with Dali/FSSP , 1998, Nucleic Acids Res..

[64]  Sean R. Eddy,et al.  Pfam: multiple sequence alignments and HMM-profiles of protein domains , 1998, Nucleic Acids Res..

[65]  A. Bairoch,et al.  The PROSITE database, its status in 1997 , 1997, Nucleic Acids Res..

[66]  W R Taylor,et al.  SSAP: sequential structure alignment program for protein structure comparison. , 1996, Methods in enzymology.

[67]  Vladimir Vapnik,et al.  The Nature of Statistical Learning , 1995 .

[68]  S Kullback,et al.  LETTER TO THE EDITOR: THE KULLBACK-LEIBLER DISTANCE , 1987 .

[69]  K Henrick,et al.  Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions , 2022 .

[70]  H. Berman,et al.  Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank , 2022 .