ProtIdent: a web server for identifying proteases and their types by fusing functional domain and sequential evolution information.

[1]  Neil D. Rawlings,et al.  MEROPS: the peptidase database , 2009, Nucleic Acids Res..

[2]  Hao Lin.  The modified Mahalanobis Discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition. , 2008, Journal of theoretical biology.

[3]  Lourdes Santana,et al.  Proteomics, networks and connectivity indices , 2008, Proteomics.

[4]  K. Chou,et al.  Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms , 2008, Nature Protocols.

[5]  K. Chou,et al.  Recent progress in protein subcellular location prediction. , 2007, Analytical biochemistry.

[6]  Zhanchao Li,et al.  Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes. , 2007, Journal of theoretical biology.

[7]  Thorsteinn Rögnvaldsson,et al.  Bioinformatic approaches for modeling the substrate specificity of HIV-1 protease: an overview , 2007, Expert review of molecular diagnostics.

[8]  Narmada Thanki,et al.  CDD: a conserved domain database for interactive domain family analysis , 2006, Nucleic Acids Res..

[9]  G. Liang,et al.  A new sequence representation as applied in better specificity elucidation for human immunodeficiency virus type 1 protease. , 2007, Biopolymers.

[10]  Kuo-Chen Chou,et al.  Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest Neighbor classifiers. , 2006, Journal of proteome research.

[11]  Yu-Dong Cai,et al.  Predicting protease types by hybridizing gene ontology and pseudo amino acid composition , 2006, Proteins.

[12]  Kuo-Chen Chou,et al.  Prediction of protease types in a hybridization space. , 2006, Biochemical and biophysical research communications.

[13]  Peer Bork,et al.  SMART 5: domains in the context of genomes and networks , 2005, Nucleic Acids Res..

[14]  Robert D. Finn,et al.  Pfam: clans, web tools and services , 2005, Nucleic Acids Res..

[15]  Thorsteinn S. Rögnvaldsson,et al.  Comprehensive Bioinformatic Analysis of the Specificity of Human Immunodeficiency Virus Type 1 Protease , 2005, Journal of Virology.

[16]  K. Chou.  Structural bioinformatics and its impact to biomedical science. , 2004, Current medicinal chemistry.

[17]  Kuo-Chen Chou,et al.  Erratum to “Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS” [Biochem. Biophys. Res. Commun. 308 (2003) 148–151] , 2003, Biochemical and Biophysical Research Communications.

[18]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[19]  Kuo-Chen Chou,et al.  Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS , 2003, Biochemical and Biophysical Research Communications.

[20]  X. Puente,et al.  Human and mouse proteases: a comparative genomic approach , 2003, Nature Reviews Genetics.

[21]  K. Chou,et al.  Using Functional Domain Composition and Support Vector Machines for Prediction of Protein Subcellular Location* , 2002, The Journal of Biological Chemistry.

[22]  Thomas L. Madden,et al.  Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. , 2001, Nucleic acids research.

[23]  K. Chou.  Prediction of protein cellular attributes using pseudo‐amino acid composition , 2001, Proteins.

[24]  K. Chou.  Prediction of protein cellular attributes using pseudo‐amino acid composition , 2001 .

[25]  A. Tomasselli,et al.  The atomic-resolution structure of human caspase-8, a key activator of apoptosis. , 1999, Structure.

[26]  Emad S. Alnemri,et al.  Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1 , 1999, Nature.

[27]  Junying Yuan,et al.  Solution Structure of BID, an Intracellular Amplifier of Apoptotic Signaling , 1999, Cell.

[28]  C. Seife.  Blunting Nature's Swiss Army Knife , 1997, Science.

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

[30]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL , 1997, Nucleic Acids Res..

[31]  K. Chou.  Prediction of human immunodeficiency virus protease cleavage sites in proteins. , 1996, Analytical biochemistry.

[32]  Thierry Denoeux,et al.  A k-nearest neighbor classification rule based on Dempster-Shafer theory , 1995, IEEE Trans. Syst. Man Cybern..

[33]  K. Chou,et al.  A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. , 1993, The Journal of biological chemistry.

[34]  A. Tomasselli,et al.  A cumulative specificity model for proteases from human immunodeficiency virus types 1 and 2, inferred from statistical analysis of an extended substrate data base. , 1991, The Journal of biological chemistry.

[35]  A. Barrett,et al.  Nomenclature: protease, proteinase and peptidase. , 1986, The Biochemical journal.

[36]  K Nishikawa,et al.  The folding type of a protein is relevant to the amino acid composition. , 1986, Journal of biochemistry.

[37]  Forest Baskett,et al.  An Algorithm for Finding Nearest Neighbors , 1975, IEEE Transactions on Computers.