COMPUTATIONAL ANALYSIS OF 3D PROTEIN STRUCTURES
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[1] Kian-Lee Tan,et al. Ppiclust: Efficient Clustering of 3D protein-protein Interaction Interfaces , 2008, J. Bioinform. Comput. Biol..
[2] David T. Jones,et al. Bioinformatics: Genes, Proteins and Computers , 2007 .
[3] Xianggui Qu,et al. Multivariate Data Analysis , 2007, Technometrics.
[4] Kian-Lee Tan,et al. Matalign: Precise Protein Structure Comparison by Matrix Alignment , 2006, J. Bioinform. Comput. Biol..
[5] Sang Joon Kim,et al. A Mathematical Theory of Communication , 2006 .
[6] Kian-Lee Tan,et al. Automatic 3D Protein Structure Classification without Structural Alignment , 2005, J. Comput. Biol..
[7] Ruth Nussinov,et al. Generation and analysis of a protein–protein interface data set with similar chemical and spatial patterns of interactions , 2005, Proteins.
[8] Kian-Lee Tan,et al. Towards Scaleable Protein Structure Comparison and Database Search , 2005, Int. J. Artif. Intell. Tools.
[9] J. Gibrat,et al. Protein secondary structure assignment revisited: a detailed analysis of different assignment methods , 2005, BMC Structural Biology.
[10] Wei Wang,et al. Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs , 2005, J. Comput. Biol..
[11] Michael A. Erdmann,et al. Protein Similarity from Knot Theory: Geometric Convolution and Line Weavings , 2005, J. Comput. Biol..
[12] Feng Gao,et al. PSIST: indexing protein structures using suffix trees , 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).
[13] Douglas B. Kell,et al. Computational cluster validation in post-genomic data analysis , 2005, Bioinform..
[14] Craig A. Stewart,et al. Introduction to computational biology , 2005 .
[15] Bing-Yu Chen,et al. A web-based three-dimensional protein retrieval system by matching visual similarity , 2005, Bioinform..
[16] Ozlem Keskin,et al. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces , 2005, Bioinform..
[17] Ambuj K. Singh,et al. Decision Tree Based Information Integration for Automated Protein Classification , 2005, J. Bioinform. Comput. Biol..
[18] Fred P. Davis,et al. PIBASE: a comprehensive database of structurally defined protein interfaces , 2005, Bioinform..
[19] Rachel Kolodny,et al. Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. , 2005, Journal of molecular biology.
[20] Zhiping Weng,et al. FAST: A novel protein structure alignment algorithm , 2004, Proteins.
[21] Cathy H. Wu,et al. The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..
[22] Zi Huang,et al. High dimensional indexing for protein structure matching using bowties , 2005, APBC.
[23] Chung-Ming Chen,et al. Classification of protein 3D folds by hidden Markov learning on sequences of structural alphabets , 2005, APBC.
[24] Michael Lanzer,et al. The Malarial Secretome , 2004, Science.
[25] K Henrick,et al. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. , 2004, Acta crystallographica. Section D, Biological crystallography.
[26] Berrin A. Yanikoglu,et al. Protein Structural Class Determination Using Support Vector Machines , 2004, ISCIS.
[27] Ruth Nussinov,et al. Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations , 2004, WABI.
[28] Keun Ho Ryu,et al. Fast Similarity Search for Protein 3D Structure Databases Using Spatial Topological Patterns , 2004, DEXA.
[29] Keun Ho Ryu,et al. Effective Filtering for Structural Similarity Search in Protein 3D Structure Databases , 2004, DEXA.
[30] Dmitrii A. Polshakov,et al. A New Approach to Protein Structure Mining and Alignment , 2004, BIOKDD.
[31] Iosif I Vaisman,et al. A simple topological representation of protein structure: Implications for new, fast, and robust structural classification , 2004, Proteins.
[32] Robert D. Carr,et al. 1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap , 2004, J. Comput. Biol..
[33] Eyke Hüllermeier,et al. Efficient similarity search in protein structure databases by k-clique hashing , 2004, Bioinform..
[34] S Miyano,et al. Open source clustering software. , 2004, Bioinformatics.
[35] Stella Veretnik,et al. Toward consistent assignment of structural domains in proteins. , 2004, Journal of molecular biology.
[36] Kian-Lee Tan,et al. Automatic protein structure classification through structural fingerprinting , 2004, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering.
[37] See-Kiong Ng,et al. Discovering novel interacting motif pairs from large protein-protein interaction datasets , 2004, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering.
[38] Kian-Lee Tan,et al. Rapid 3D protein structure database searching using information retrieval techniques , 2004, Bioinform..
[39] H. Wolfson,et al. Recognition of Functional Sites in Protein Structures☆ , 2004, Journal of Molecular Biology.
[40] H. Wolfson,et al. A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications , 2004, Protein science : a publication of the Protein Society.
[41] Anthony K. H. Tung,et al. Substructure clustering on sequential 3d object datasets , 2004, Proceedings. 20th International Conference on Data Engineering.
[42] Sung-Hou Kim,et al. Local feature frequency profile: a method to measure structural similarity in proteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[43] Ambuj K. Singh,et al. Index-based Similarity Search for Protein Structure Databases , 2004, J. Bioinform. Comput. Biol..
[44] W. Pearson,et al. Sensitivity and selectivity in protein structure comparison , 2004, Protein science : a publication of the Protein Society.
[45] Dinesh Gupta,et al. Distribution of proline-rich (PxxP) motifs in distinct proteomes: functional and therapeutic implications for malaria and tuberculosis. , 2004, Protein engineering, design & selection : PEDS.
[46] Jinyan Li,et al. Discovery of Binding Motif Pairs from Protein Complex Structural Data and Protein Interaction Sequence Data , 2004, Pacific Symposium on Biocomputing.
[47] A Chinnasamy,et al. Protein structure and fold prediction using tree-augmented naive Bayesian classifier. , 2004, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[48] Wei Wang,et al. Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis , 2003, Pacific Symposium on Biocomputing.
[49] Gerard J Kleywegt,et al. Evaluation of protein fold comparison servers , 2003, Proteins.
[50] Matteo Comin,et al. PROuST: a server based comparison method of three-dimensional structures of proteins using indexing techniques , 2004 .
[51] See-Kiong Ng,et al. Discovering Protein-protein Interactions , 2004, J. Bioinform. Comput. Biol..
[52] Ankush Mittal,et al. Protein Structure and Fold Prediction Using Tree-Augmented Bayesian Classifier , 2004, Pacific Symposium on Biocomputing.
[53] Z. Weng,et al. Atomic contact vectors in protein‐protein recognition , 2003, Proteins.
[54] Dan M. Bolser,et al. Visualisation and graph-theoretic analysis of a large-scale protein structural interactome , 2003, BMC Bioinformatics.
[55] Adam Godzik,et al. Flexible structure alignment by chaining aligned fragment pairs allowing twists , 2003, ECCB.
[56] Frances M. G. Pearl,et al. Recognizing the fold of a protein structure , 2003, Bioinform..
[57] B. Honig,et al. Structural genomics: Computational methods for structure analysis , 2003, Protein science : a publication of the Protein Society.
[58] Leszek Rychlewski,et al. ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins , 2003, Nucleic Acids Res..
[59] R. Nussinov,et al. Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[60] Ming-Jing Hwang,et al. Protein structure comparison by probability-based matching of secondary structure elements , 2003, Bioinform..
[61] Lin Wang,et al. Felic (CIP4b), a novel binding partner with the Src kinase Lyn and Cdc42, localizes to the phagocytic cup. , 2003, Blood.
[62] Kian-Lee Tan,et al. An efficient index-based protein structure database searching method , 2003, Eighth International Conference on Database Systems for Advanced Applications, 2003. (DASFAA 2003). Proceedings..
[63] S D O'Hearn,et al. MolCom: a method to compare protein molecules based on 3-D structural and chemical similarity. , 2003, Protein engineering.
[64] Sung-Hou Kim,et al. A global representation of the protein fold space , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[65] Ilya N. Shindyalov,et al. PDP: protein domain parser , 2003, Bioinform..
[66] Sung-Hou Kim,et al. Overview of structural genomics: from structure to function. , 2003, Current opinion in chemical biology.
[67] U. Bastolla,et al. Testing similarity measures with continuous and discrete protein models , 2002, Proteins.
[68] Dan M. Bolser,et al. Fast and efficient computation of domain-domaininteractions from known protein structures in the PDB , 2003, German Conference on Bioinformatics.
[69] Giuseppe Lancia,et al. Protein Structure Comparison: Algorithms and Applications , 2003, Mathematical Methods for Protein Structure Analysis and Design.
[70] 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.
[71] Adam Godzik,et al. The neaning and limitations of protein structure alignments , 2002, Proceedings. First International Symposium on 3D Data Processing Visualization and Transmission.
[72] Osvaldo Olmea,et al. MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison , 2002, Protein science : a publication of the Protein Society.
[73] B. Snel,et al. Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.
[74] J. Janin,et al. Dissecting protein–protein recognition sites , 2002, Proteins.
[75] David Eisenberg,et al. GXXXG and AXXXA: Common α-Helical Interaction Motifs in Proteins, Particularly in Extremophiles† , 2002 .
[76] Bonnie Berger,et al. trilogy: Discovery of sequence–structure patterns across diverse proteins , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[77] Bertil Schmidt,et al. Massively parallel solutions for molecular sequence analysis , 2002, Proceedings 16th International Parallel and Distributed Processing Symposium.
[78] William R Taylor,et al. Protein Structure Comparison Using Bipartite Graph Matching and Its Application to Protein Structure Classification * , 2002, Molecular & Cellular Proteomics.
[79] A. Valencia,et al. Prediction of protein--protein interaction sites in heterocomplexes with neural networks. , 2002, European journal of biochemistry.
[80] S. Pongor,et al. Protein fold similarity estimated by a probabilistic approach based on Cα-Cα distance comparison , 2002 .
[81] Margaret H. Dunham,et al. Data Mining: Introductory and Advanced Topics , 2002 .
[82] S. Pongor,et al. Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison. , 2002, Journal of molecular biology.
[83] A. Gronenborn,et al. Core mutations switch monomeric protein GB1 into an intertwined tetramer , 2002, Nature Structural Biology.
[84] Petra Perner,et al. Data Mining - Concepts and Techniques , 2002, Künstliche Intell..
[85] Hugh E. Williams,et al. Indexing and Retrieval for Genomic Databases , 2002, IEEE Trans. Knowl. Data Eng..
[86] David Eisenberg,et al. GXXXG and AXXXA: common alpha-helical interaction motifs in proteins, particularly in extremophiles. , 2002, Biochemistry.
[87] Olivier Lichtarge,et al. Getting past appearances: the many-fold consequences of remote homology , 2001, Nature Structural Biology.
[88] S. Brenner. A tour of structural genomics , 2001, Nature Reviews Genetics.
[89] E. Sprinzak,et al. Correlated sequence-signatures as markers of protein-protein interaction. , 2001, Journal of molecular biology.
[90] S. Sitharama Iyengar,et al. Content based image retrieval and information theroy: a general approach , 2001 .
[91] P. Koehl,et al. Protein structure similarities. , 2001, Current opinion in structural biology.
[92] R Nussinov,et al. Automated multiple structure alignment and detection of a common substructural motif , 2001, Proteins.
[93] Chris H. Q. Ding,et al. Multi-class protein fold recognition using support vector machines and neural networks , 2001, Bioinform..
[94] Jong H. Park,et al. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. , 2001, Journal of molecular biology.
[95] S. Sitharama Iyengar,et al. Content based image retrieval and information theory: A general approach , 2001, J. Assoc. Inf. Sci. Technol..
[96] William R. Taylor,et al. Structure Motif Discovery and Mining the PDB , 2002, German Conference on Bioinformatics.
[97] Andrew J. Martin,et al. The ups and downs of protein topology; rapid comparison of protein structure. , 2000, Protein engineering.
[98] K. Nishikawa,et al. Protein structure comparison using the Markov transition model of evolution , 2000, Proteins.
[99] 김삼묘,et al. “Bioinformatics” 특집을 내면서 , 2000 .
[100] Liisa Holm,et al. DaliLite workbench for protein structure comparison , 2000, Bioinform..
[101] R. Nussinov,et al. Conservation of polar residues as hot spots at protein interfaces , 2000, Proteins.
[102] J. Rosamond,et al. Harnessing the power of the genome in the search for new antibiotics. , 2000, Science.
[103] J. Szustakowski,et al. Protein structure alignment using a genetic algorithm , 2000, Proteins.
[104] D. Engelman,et al. The GxxxG motif: a framework for transmembrane helix-helix association. , 2000, Journal of molecular biology.
[105] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[106] William R. Taylor,et al. Structure Comparison and Structure Patterns , 2000, J. Comput. Biol..
[107] Patrice Koehl,et al. The ASTRAL compendium for protein structure and sequence analysis , 2000, Nucleic Acids Res..
[108] C. Orengo. CORA—Topological fingerprints for protein structural families , 2008, Protein science : a publication of the Protein Society.
[109] T. Ohkawa,et al. A method of comparing protein structures based on matrix representation of secondary structure pairwise topology , 1999, Proceedings 1999 International Conference on Information Intelligence and Systems (Cat. No.PR00446).
[110] Ole Lund,et al. MatrixPlot: visualizing sequence constraints , 1999, Bioinform..
[111] Thierry Pun,et al. Efficient access methods for content-based image retrieval with inverted files , 1999, Optics East.
[112] Martin Reczko,et al. Protein Fold Class Prediction: New Methods of Statistical Classification , 1999, ISMB.
[113] Hans-Peter Kriegel,et al. 3D Shape Histograms for Similarity Search and Classification in Spatial Databases , 1999, SSD.
[114] David R. Gilbert,et al. Motif-based searching in TOPS protein topology databases , 1999, Bioinform..
[115] C. Chothia,et al. The atomic structure of protein-protein recognition sites. , 1999, Journal of molecular biology.
[116] B. Rost. Twilight zone of protein sequence alignments. , 1999, Protein engineering.
[117] C Sander,et al. Dictionary of recurrent domains in protein structures , 1998, Proteins.
[118] P E Bourne,et al. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.
[119] Hans-Jörg Schek,et al. A Quantitative Analysis and Performance Study for Similarity-Search Methods in High-Dimensional Spaces , 1998, VLDB.
[120] A. Bogan,et al. Anatomy of hot spots in protein interfaces. , 1998, Journal of molecular biology.
[121] 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.
[122] Hans-Peter Kriegel,et al. Similarity Search in 3D Protein Databases , 1998, German Conference on Bioinformatics.
[123] Tim J. P. Hubbard,et al. SCOP: a structural classification of proteins database , 1998, Nucleic Acids Res..
[124] Haim J. Wolfson,et al. Geometric hashing: an overview , 1997 .
[125] Ruth Nussinov,et al. Structural motifs at protein‐protein interfaces: Protein cores versus two‐state and three‐state model complexes , 1997, Protein science : a publication of the Protein Society.
[126] Elisa Bertino,et al. Indexing Techniques for Advanced Database Systems , 1997, The Springer International Series on Advances in Database Systems.
[127] David C. Jones,et al. CATH--a hierarchic classification of protein domain structures. , 1997, Structure.
[128] Douglas L. Brutlag,et al. Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations , 1997, ISMB.
[129] Thomas Lengauer,et al. Detection of Distant Structural Similarities in a Set of Proteins Using a Fast Graph-Based Method , 1997, ISMB.
[130] G. Kleywegt,et al. Detecting folding motifs and similarities in protein structures. , 1997, Methods in enzymology.
[131] R Abagyan,et al. Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search , 1997, Proteins.
[132] Benjamin W. Wah,et al. Editorial: Two Named to Editorial Board of IEEE Transactions on Knowledge and Data Engineering , 1996 .
[133] H. Wolfson,et al. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. , 1996, Journal of molecular biology.
[134] D Fischer,et al. Analysis of topological and nontopological structural similarities in the PDB: New examples with old structures , 1996, Proteins.
[135] A. Godzik. The structural alignment between two proteins: Is there a unique answer? , 1996, Protein science : a publication of the Protein Society.
[136] G. Kleywegt. Use of non-crystallographic symmetry in protein structure refinement. , 1996, Acta crystallographica. Section D, Biological crystallography.
[137] Mark Gerstein,et al. Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures , 1996, ISMB.
[138] J F Gibrat,et al. Surprising similarities in structure comparison. , 1996, Current opinion in structural biology.
[139] F. Cohen,et al. A surface of minimum area metric for the structural comparison of proteins. , 1996, Journal of molecular biology.
[140] M J Sippl,et al. Optimum superimposition of protein structures: ambiguities and implications. , 1996, Folding & design.
[141] George D. Rose,et al. No Assembly Required , 1996 .
[142] C. Chothia,et al. Understanding protein structure: using scop for fold interpretation. , 1996, Methods in enzymology.
[143] A Elofsson,et al. Assessing the performance of fold recognition methods by means of a comprehensive benchmark. , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[144] Chris Sander,et al. 3-D Lookup: Fast Protein Structure Database Searches at 90% Reliability , 1995, ISMB.
[145] P. Argos,et al. Knowledge‐based protein secondary structure assignment , 1995, Proteins.
[146] R. Nussinov,et al. A 3D sequence-independent representation of the protein data bank. , 1995, Protein engineering.
[147] Michael S. Waterman,et al. Introduction to computational biology , 1995 .
[148] Tatsuya Akutsu. Protein Structure Alignment Using a Graph Matching Technique , 1995 .
[149] C. Sander,et al. The FSSP database of structurally aligned protein fold families. , 1994, Nucleic acids research.
[150] C. Sander,et al. Searching protein structure databases has come of age , 1994, Proteins.
[151] C. Sander,et al. Parser for protein folding units , 1994, Proteins.
[152] D. Goodman. Personal Communications , 1994, Mobile Communications.
[153] C. Sander,et al. Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.
[154] D Fischer,et al. A computer vision based technique for 3-D sequence-independent structural comparison of proteins. , 1993, Protein engineering.
[155] M. Levitt,et al. Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core , 1993, Current Biology.
[156] P Willett,et al. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. , 1993, Journal of molecular biology.
[157] H. Wolfson,et al. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[158] Peter J. Rousseeuw,et al. Finding Groups in Data: An Introduction to Cluster Analysis , 1990 .
[159] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[160] T. Blundell,et al. Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. , 1990, Journal of molecular biology.
[161] W R Taylor,et al. Protein structure alignment. , 1989, Journal of molecular biology.
[162] Gordon M. Crippen,et al. Distance Geometry and Molecular Conformation , 1988 .
[163] S Rackovsky,et al. Protein comparison and classification: a differential geometric approach. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[164] K. S. Arun,et al. Least-Squares Fitting of Two 3-D Point Sets , 1987, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[165] F. Critchley,et al. Multivariate Data Analysis , 1988 .
[166] Temple F. Smith,et al. Comparison of biosequences , 1981 .
[167] W. Kabsch. A discussion of the solution for the best rotation to relate two sets of vectors , 1978 .
[168] P Argos,et al. Exploring structural homology of proteins. , 1976, Journal of molecular biology.
[169] E. Padlan,et al. Variability of three-dimensional structure in immunoglobulins. , 1975, Proceedings of the National Academy of Sciences of the United States of America.
[170] C. Epstein,et al. The reversible reduction of disulfide bonds in trypsin and ribonuclease coupled to carboxymethyl cellulose. , 1962, The Journal of biological chemistry.
[171] Journal of Molecular Biology , 1959, Nature.
[172] G. Giacomello,et al. Proteins structure. , 1957, Scientia medica italica. English ed.
[173] A. I.,et al. Neural Field Continuum Limits and the Structure–Function Partitioning of Cognitive–Emotional Brain Networks , 2023, Biology.
[174] Bernard S. Wostmann,et al. Panel of referees , 2007 .
[175] Christus,et al. A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 2022 .