Impacts of bioinformatics to medicinal chemistry

Medicinal Chemistry

Volumn 11, Issue 3, 2015, Pages 218-234

  Chou, Kuo Chen ^a,b  

^a GORDON LIFE SCIENCE INSTITUTE   (United States)

^b KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

Distorted key theory and peptide drugs; Drug and target protein interaction; Graphical rules; Multi label systems; PseAAC; PseKNC; Wenxiang diagram

Indexed keywords

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CELLULAR DISTRIBUTION; GENOME ANALYSIS; MEDICINAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; RNA SEQUENCE; ANIMAL; BIOLOGY; CHEMISTRY; HUMAN; SYNTHESIS;

PEPTIDE;

ANIMALS; CHEMISTRY, PHARMACEUTICAL; COMPUTATIONAL BIOLOGY; HUMANS; PEPTIDES;

EID: 84926619444     PISSN: 15734064     EISSN: 18756638     Source Type: Journal    
DOI: 10.2174/1573406411666141229162834     Document Type: Article

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126. Chen, W.; Feng, P.M.; Deng, E.Z.; Lin, H.; Chou, K.C. iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition. Anal. Biochem., 2014, 462, 76-83.
127. Lin, H.; Deng, E.Z.; Ding, H.; Chen, W.; Chou, K.C. iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition. Nucleic Acids Res., 2014, 42, 12961-12972.
128. Chen, W.; Zhang, X.; Brooker, J.; Lin, H.; Zhang, L.; Chou, K.C. PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions. Bioinformatics, 2015, 31, 119-120.
129. Liu, B.; Liu, F.; Fang, L.; Wang, X.; Chou, K.C. repDNA: a Python package to generate various features of DNA sequences incorporating physicochemical properties and sequence-order effects. Bioinformatics, 2015, doi: 10.1093/bioinformatics/btu1820.
130. Shen, H.B.; Chou, K.C. Hum-mPLoc: An ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites. Biochem. Biophys. Res. Commun. (BBRC), 2007, 355, 1006-1011.
131. Chou, K.C.; Shen, H.B. Cell-PLoc: A package of Web servers for predicting subcellular localization of proteins in various organisms. Nat. Protocols, 2008, 3, 153-162.
132. Chou, K.C.; Shen, H.B. Review: Recent progresses in protein subcellular location prediction. Anal. Biochem., 2007, 370, 1-16.
133. Chou, K.C. Some Remarks on Predicting Multi-Label Attributes in Molecular Biosystems. Mol. Biosyst., 2013, 9, 1092-1100.
134. Chou, K.C.; Shen, H.B. Cell-PLoc 2.0: An improved package of web-servers for predicting subcellular localization of proteins in various organisms. Nat. Sci., 2010, 2, 1090-1103.
135. Chen, L.; Zeng, W.M.; Cai, Y.D.; Feng, K.Y.; Chou, K.C. Predicting Anatomical Therapeutic Chemical (ATC) classification of drugs by integrating chemical-chemical interactions and similarities. PLoS One, 2012, 7, e35254.
136. Chou, K.C.; Jiang, S.P.; Liu, W.M.; Fee, C.H. Graph theory of enzyme kinetics: 1. Steady-state reaction system. Sci. Sinica, 1979, 22, 341-358.
137. Chou, K.C.; Liu, W.M. Graphical rules for non-steady state enzyme kinetics. J. Theor. Biol., 1981, 91, 637-654.
138. Chou, K.C.; Forsen, S. Graphical rules for enzyme-catalyzed rate laws. Biochem. J., 1980, 187, 829-835.
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140. Chou, K.C. A new schematic method in enzyme kinetics. Eur. J. Biochem., 1980, 113, 195-198.
141. Chou, K.C. Two new schematic rules for rate laws of enzyme-catalyzed reactions. J. Theor. Biol., 1981, 89, 581-592.
142. Zhou, G.P.; Deng, M.H. An extension of Chou's graphic rules for deriving enzyme kinetic equations to systems involving parallel reaction pathways. Biochem. J., 1984, 222, 169-176.
143. Myers, D.; Palmer, G. Microcomputer tools for steady-state enzyme kinetics. Bioinformatics (original: Computer Applied Bioscience), 1985, 1, 105-110.
144. Chou, K.C. Graphic rules in steady and non-steady enzyme kinetics. J. Biol. Chem., 1989, 264, 12074-12079.
145. Andraos, J. Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws: new methods based on directed graphs. Can. J. Chem., 2008, 86, 342-357.
146. Chou, K.C. Review: Applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady state systems. Biophys. Chem., 1990, 35, 1-24.
147. Shen, H.B.; Song, J.N.; Chou, K.C. Prediction of protein folding rates from primary sequence by fusing multiple sequential features. J. Biom. Sci. Eng., 2009, 2, 136-143.
148. Chou, K.C.; Shen, H.B. FoldRate: A web-server for predicting protein folding rates from primary sequence. Open Bioinformatics J., 2009, 3, 31-50.
149. Althaus, I.W.; Chou, J.J.; Gonzales, A.J.; Diebel, M.R.; Chou, K.C.; Kezdy, F.J.; Romero, D.L.; Aristoff, P.A.; Tarpley, W.G.; Reusser, F. Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E. J. Biol. Chem., 1993, 268, 6119-6124.
150. Althaus, I.W.; Gonzales, A.J.; Chou, J.J.; Diebel, M.R.; Chou, K.C.; Kezdy, F.J.; Romero, D.L.; Aristoff, P.A.; Tarpley, W.G.; Reusser, F. The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase. J. Biol. Chem., 1993, 268, 14875-14880.
151. Althaus, I.W.; Chou, J.J.; Gonzales, A.J.; Diebel, M.R.; Chou, K.C.; Kezdy, F.J.; Romero, D.L.; Aristoff, P.A.; Tarpley, W.G.; Reusser, F. Kinetic studies with the nonnucleoside HIV-1 reverse transcriptase inhibitor U-88204E. Biochemistry, 1993, 32, 6548-6554.
152. Althaus, I.W.; Chou, J.J.; Gonzales, A.J.; Diebel, M.R.; Chou, K.C.; Kezdy, F.J.; Romero, D.L.; Aristoff, P.A.; Tarpley, W.G.; Reusser, F. Steady-state kinetic studies with the polysulfonate U-9843, an HIV reverse transcriptase inhibitor. Experientia, 1994, 50, 23-28.
153. Althaus, I.W.; Chou, J.J.; Gonzales, A.J.; Diebel, M.R.; Chou, K.C.; Kezdy, F.J.; Romero, D.L.; Thomas, R.C.; Aristoff, P.A.; Tarpley, W.G.; Reusser, F. Kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-90152E. Biochem. Pharmacol., 1994, 47, 2017-2028.
154. Althaus, I.W.; Chou, K.C.; Franks, K.M.; Diebel, M.R.; Kezdy, F.J.; Romero, D.L.; Thomas, R.C.; Aristoff, P.A.; Tarpley, W.G.; Reusser, F. The benzylthio-pyrididine U-31, 355 is a potent inhibitor of HIV-1 reverse transcriptase. Biochem. Pharmacol., 1996, 51, 743-750.
155. Qiu, W.R.; Xiao, X.; Lin, W.Z.; Chou, K.C. iUbiq-Lys: Prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a grey system model Journal of Bio-molecular Structure and Dynamics (JBSD) 2014, doi:10.1080/07391102.2014.968875.
156. Liu, Z.; Xiao, X.; Qiu, W.R.; Chou, K.C. iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition. Anal. Biochem., 2015, ihttp://dx.doi.org/10.1016/j.ab.2014.12.009.
157. Chou, K.C. Graphic rule for drug metabolism systems. Curr. Drug Metab., 2010, 11, 369-378.
158. Chou, K.C.; Zhang, C.T. Diagrammatization of codon usage in 339 HIV proteins and its biological implication. AIDS Res. Human Retroviruses, 1992, 8, 1967-1976.
159. Zhang, C.T.; Chou, K.C. Graphic analysis of codon usage strategy in 1490 human proteins. J. Protein Chem., 1993, 12, 329-335.
160. Zhang, C.T.; Chou, K.C. Analysis of codon usage in 1562 E. Coli protein coding sequences. J. Mol. Biol., 1994, 238, 1-8.
161. Chou, K.C.; Zhang, C.T.; Elrod, D.W. Do antisense proteins exist? J. Protein Chem., 1996, 15, 59-61.
162. Wu, Z.C.; Xiao, X.; Chou, K.C. 2D-MH: A web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids. J. Theor. Biol., 2010, 267, 29-34.
163. Xie, G.; Mo, Z. Three 3D graphical representations of DNA primary sequences based on the classifications of DNA bases and their applications. J. Theor. Biol., 2011, 269, 123-130.
164. Yu, J.F.; Sun, X.; Wang, J.H. TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications. J. Theor. Biol., 2009, 261, 459-468.
165. Chou, K.C.; Lin, W.Z.; Xiao, X. Wenxiang: a web-server for drawing wenxiang diagrams Natural Science, 2011, 3, 862-865.
166. Zhou, G.P. The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein-protein interaction mechanism. J. Theor. Biol., 2011, 284, 142-148.
167. Zhou, G.P. The Structural determinations of the leucine zipper coiled-coil domains of the cGMP-dependent protein kinase I alpha and its interaction with the myosin binding subunit of the myosin light chains phosphase. Proteins Pept. Lett., 2011, 18, 966-978.
168. Zhou, G.P.; Huang, R.B. The pH-Triggered Conversion of the PrP(c) to PrP(sc.). Curr. Top. Med. Chem., 2013, 13, 1152-1163.
169. Gonzalez-Diaz, H.; Perez-Montoto, L.G.; Duardo-Sanchez, A.; Paniagua, E.; Vazquez-Prieto, S.; Vilas, R.; Dea-Ayuela, M.A.; Bolas-Fernandez, F.; Munteanu, C.R.; Dorado, J.; Costas, J.; Ubeira, F.M. Generalized lattice graphs for 2D-visualization of biological information. J. Theor. Biol., 2009, 261, 136-147.
170. Munteanu, C.R.; Magalhaes, A.L.; Uriarte, E.; Gonzalez-Diaz, H. Multi-target QPDR classification model for human breast and colon cancer-related proteins using star graph topological indices. J. Theor. Biol., 2009, 257, 303-311.
171. Shen, Y.Z.; Ding, Y.S.; Gu, Q.; Chou, K.C. Identifying the hub proteins from complicated membrane protein network systems. Med. Chem., 2010, 6, 165-173.
172. Wolfram, S. Cellular automation as models of complexity. Nature, 1984, 311, 419-424.
173. Wolfram, S. A New Kind of Science; Wolfram Media Inc.: Champaign, IL, 2002.
174. Xiao, X.; Shao, S.H.; Chou, K.C. A probability cellular automaton model for hepatitis B viral infections. Biochem. Biophys. Res. Comm. (BBRC), 2006, 342, 605-610.
175. Xiao, X.; Shao, S.; Ding, Y.; Huang, Z.; Chen, X.; Chou, K.C. An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation. J. Theor. Biol., 2005, 235, 555-565.
176. Wang, M.; Yao, J.S.; Huang, Z.D.; Xu, Z.J.; Liu, G.P.; Zhao, H.Y.; Wang, X.Y.; Yang, J.; Zhu, Y.S.; Chou, K.C. A new nucleotide-composition based fingerprint of SARS-CoV with visualization analysis. Med. Chem., 2005, 1, 39-47.
177. Xiao, X.; Shao, S.; Ding, Y.; Huang, Z.; Chen, X.; Chou, K.C. Using cellular automata to generate Image representation for biological sequences. Amino Acids, 2005, 28, 29-35.
178. Xiao, X.; Wang, P.; Chou, K.C. GPCR-CA: A cellular automaton image approach for predicting G-protein-coupled receptor functional classes. J. Comput. Chem., 2009, 30, 1414-1423.
179. Knowles, J.; Gromo, G. A guide to drug discovery: Target selection in drug discovery. Nat. Rev. Drug Discov., 2003, 2, 63-69.
180. Lindsay, M.A. Target discovery. Nat. Rev. Drug Discov., 2003, 2, 831-838.
181. Chou, K.C.; Wei, D.Q.; Zhong, W.Z. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. (Erratum: ibid., 2003, Vol.310, 675). Biochem. Biophys. Res. Comm. (BBRC), 2003, 308, 148-151.
182. Zhou, G.P.; Troy, F.A. NMR studies on how the binding complex of polyisoprenol recognition sequence peptides and polyisoprenols can modulate membrane structure. Curr. Protein Pept. Sci., 2005, 6, 399-411.
183. Chou, K.C.; Wei, D.Q.; Du, Q.S.; Sirois, S.; Zhong, W.Z. Review: Progress in computational approach to drug development against SARS. Curr. Med. Chem., 2006, 13, 3263-3270.
184. Du, Q.S.; Wang, S.; Wei, D.Q.; Sirois, S.; Chou, K.C. Molecular modelling and chemical modification for finding peptide inhibitor against SARS CoV Mpro. Anal. Biochem., 2005, 337, 262-270.
185. Huang, R.B.; Du, Q.S.; Wang, C.H.; Chou, K.C. An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus. Biochem. Biophys. Res. Comm. (BBRC), 2008, 377, 1243-1247.
186. Du, Q.S.; Huang, R.B.; Wang, C.H.; Li, X.M.; Chou, K.C. Energetic analysis of the two controversial drug binding sites of the M2 proton channel in influenza A virus. J. Theor. Biol., 2009, 259, 159-164.
187. Wei, H.; Wang, C.H.; Du, Q.S.; Meng, J.; Chou, K.C. Investigation into adamantane-based M2 inhibitors with FB-QSAR. Med. Chem, 2009, 5, 305-317.
188. Du, Q.S.; Huang, R.B.; Wang, S.Q.; Chou, K.C. Designing inhibitors of M2 proton channel against H1N1 swine influenza virus. PLoS One, 2010, 5, e9388.
189. Wang, S.Q.; Du, Q.S.; Huang, R.B.; Zhang, D.W.; Chou, K.C. Insights from investigating the interaction of oseltamivir (Tamiflu) with neuraminidase of the 2009 H1N1 swine flu virus. Biochem. Biophys. Res. Commun. (BBRC), 2009, 386, 432-436.
190. Chou, K.C. Review: Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11, 2105-2134.
191. Cai, L.; Wang, Y.; Wang, J.F.; Chou, K.C. Identification of proteins interacting with human SP110 during the process of viral infections. Med. Chem., 2011, 7, 121-126.
192. Liao, Q.H.; Gao, Q.Z.; Wei, J.; Chou, K.C. Docking and molecular dynamics study on the inhibitory activity of novel inhibitors on epidermal growth factor receptor (EGFR). Med. Chem., 2011, 7, 24-31.
193. Li, X.B.; Wang, S.Q.; Xu, W.R.; Wang, R.L.; Chou, K.C. Novel inhibitor design for hemagglutinin against H1N1 influenza virus by core hopping method. PLoS One, 2011, 6, e28111.
194. Ma, Y.; Wang, S.Q.; Xu, W.R.; Wang, R.L.; Chou, K.C. Design novel dual agonists for treating type-2 diabetes by targeting peroxisome proliferator-activated receptors with core hopping approach. PLoS One, 2012, 7, e38546.
195. Wang, J.F.; Chou, K.C. Insights from modeling the 3D structure of New Delhi metallo-beta-lactamase and its binding interactions with antibiotic drugs. PLoS One 2011, 6, e18414.
196. Wang, J.F.; Chou, K.C. Insights into the Mutation-Induced HHH syndrome from modeling human mitochondrial ornithine transporter-1. PLoS One, 2012, 7, e31048.
197. Berardi, M.J.; Shih, W.M.; Harrison, S.C.; Chou, J.J. Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching. Nature, 2011, 476, 109-113.
198. Schnell, J.R.; Chou, J.J. Structure and mechanism of the M2 proton channel of influenza A virus. Nature, 2008, 451, 591-595.
199. OuYang, B.; Xie, S.; Berardi, M.J.; Zhao, X.M.; Dev, J.; Yu, W.; Sun, B.; Chou, J.J. Unusual architecture of the p7 channel from hepatitis C virus. Nature 2013, 498, 521-525.
200. Oxenoid, K.; Chou, J.J. The structure of phospholamban pentamer reveals a channel-like architecture in membranes. Proc. Natl. Acad. Sci. U. S. A., 2005, 102, 10870-10875.
201. Call, M.E.; Wucherpfennig, K.W.; Chou, J.J. The structural basis for intramembrane assembly of an activating immunoreceptor complex. Nat. Immunol., 2010, 11, 1023-1029.
202. Pielak, R.M.; Chou, J.J. Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Biochem. Biophys. Res. Commun., 2010, 401, 58-63.
203. Pielak, R.M.; Jason, R. Schnell, J.R.; Chou, J.J. Mechanism of drug inhibition and drug resistance of influenza A M2 channel. Proc. Natl. Acad. Sci. U. S. A., 2009, 106, 7379-7384.
204. Wang, J.; Pielak, R.M.; McClintock, M.A.; Chou, J.J. Solution structure and functional analysis of the influenza B proton channel. Nat. Struct. Mol. Biol., 2009, 16, 1267-1271.
205. Pielak, R.M.; Chou, J.J. Influenza M2 proton channels. Biochim. Biophys. Acta, 2011, 1808, 522-529.
206. Chou, K.C.; Jones, D.; Heinrikson, R.L. Prediction of the tertiary structure and substrate binding site of caspase-8. FEBS Lett., 1997, 419, 49-54.
207. Chou, K.C.; Watenpaugh, K.D.; Heinrikson, R.L. A Model of the complex between cyclin-dependent kinase 5 (Cdk5) and the activation domain of neuronal Cdk5 activator. Biochem. Biophy. Res. Commun. (BBRC), 1999, 259, 420-428.
208. Chou, K.C.; Tomasselli, A.G.; Heinrikson, R.L. Prediction of the tertiary structure of a caspase-9/inhibitor complex. FEBS Lett., 2000, 470, 249-256.
209. Chou, K.C.; Howe, W.J. Prediction of the tertiary structure of the beta-secretase zymogen. Biochem. Biophys. Res. Commun. (BBRC), 2002, 292, 702-708.
210. Chou, K.C. Modelling extracellular domains of GABA-A receptors: subtypes 1, 2, 3, and 5. Biochem. Biophys. Res. Commun. (BBRC), 2004, 316, 636-642.
211. Chou, K.C. Insights from modelling the 3D structure of the extracellular domain of alpha7 nicotinic acetylcholine receptor. Biochem. Biophys. Res. Comm. (BBRC), 2004, 319, 433-438.
212. Chou, K.C. Molecular therapeutic target for type-2 diabetes. J. Proteome Res., 2004, 3, 1284-1288.
213. Chou, K.C. Coupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein. J. Proteome Res., 2005, 4, 1681-1686.
214. Chou, K.C. Insights from modelling three-dimensional structures of the human potassium and sodium channels. J. Proteome Res., 2004, 3, 856-861.
215. Chou, K.C. Insights from modelling the tertiary structure of BACE2. J. Proteome Res., 2004, 3, 1069-1072.
216. Chou, K.C. Insights from modeling the 3D structure of DNA-CBF3b complex. J. Proteome Res., 2005, 4, 1657-1660.
217. Chou, K.C. Modeling the tertiary structure of human cathepsin-E. Biochem. Biophys. Res. Commun. (BBRC), 2005, 331, 56-60.
218. Carlacci, L.; Chou, K.C.; Maggiora, G.M. A heuristic approach to predicting the tertiary structure of bovine somatotropin. Biochemistry, 1991, 30, 4389-4398.
219. Chou, K.C. Energy-optimized structure of antifreeze protein and its binding mechanism. J. Mol. Biol., 1992, 223, 509-517.
220. Chou, K.C.; Carlacci, L.; Maggiora, G.M.; Parodi, L.A.; Schultz, M.W. An energy-based approach to packing the 7-helix bundle of bacteriorhodopsin. Protein Sci., 1992, 1, 810-827.
221. Chou, K.C. Conformational change during photocycle of bacteriorhodopsin and its proton-pumping mechanism. J. Protein Chem., 1993, 12, 337-350.
222. Chou, K.C. The convergence-divergence duality in lectin domains of the selectin family and its implications. FEBS Lett., 1995, 363, 123-126.
223. Chou, K.C. Knowledge-based model building of tetiary structures for lectin domains of the selectin family. J. Protein Chem., 1996, 15, 161-168.
224. Chou, K.C.; Heinrikson, R.L. Prediction of the tertiary structure of the complement control protein module. J. Protein Chem., 1997, 16, 765-773.
225. Sirois, S.; Hatzakis, G.E.; Wei, D.Q.; Du, Q.S.; Chou, K.C. Assessment of chemical libraries for their druggability. Comput. Biol. Chem., 2005, 29, 55-67.
226. Xiao, X.; Min, J.L.; Wang, P.; Chou, K.C. Predict drug-protein interaction in cellular networking. Curr. Topics Med. Chem., 2013, 13, 1707-1712.
227. Min, J.L.; Xiao, X.; Chou, K.C. iEzy-Drug: A web server for identifying the interaction between enzymes and drugs in cellular networking. BioMed. Res. Int., 2013, 2013, 701317.
228. Fan, Y.N.; Xiao, X.; Min, J.L.; Chou, K.C. iNR-Drug: Predicting the interaction of drugs with nuclear receptors in cellular networking. Int. J. Mol. Sci., 2014, 15, 4915-4937.
229. Chou, K.C. Review: Progress in protein structural class prediction and its impact to bioinformatics and proteomics. Curr. Protein Pept. Sci., 2005, 6, 423-436.
230. Xiao, X.; Min, J.L.; Lin, W.Z.; Liu, Z.; Cheng, X.; Chou, K.C. iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via the benchmark dataset optimization approach. Journal of Biomolecular Structure & Dynamics (JBSD) 2014, doi: 10.1080/07391102.07392014. 07998710.
231. Chou, K.C. A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. J. Biol. Chem., 1993, 268, 16938-16948.
232. Anand, K.; Ziebuhr, J.; Wadhwani, P.; Mesters, J.R.; Hilgenfeld, R. Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science, 2003, 300, 1763-1767.
233. Chou, K.C.; Chen, N.Y.; Forsen, S. The biological functions of low-frequency phonons: 2. Cooperative effects. Chem. Scripta, 1981, 18, 126-132.
234. Chou, K.C. Review: Prediction of human immunodeficiency virus protease cleavage sites in proteins. Anal. Biochem., 1996, 233, 1-14.
235. Chou, K.C.; Tomasselli, A.L.; Reardon, I.M.; Heinrikson, R.L. Predicting HIV protease cleavage sites in proteins by a discriminant function method. Proteins: Struct., Funct., Genet., 1996, 24, 51-72.
236. Chou, J.J. Predicting cleavability of peptide sequences by HIV protease via correlation-angle approach. J. Protein Chem., 1993, 12, 291-302.
237. Zhang, C.T.; Chou, K.C. An alternate-subsite-coupled model for predicting HIV protease cleavage sites in proteins. Protein Eng., 1993, 7, 65-73.
238. Cai, Y.D.; Liu, X.J.; Xu, X.B.; Chou, K.C. Support Vector Machines for predicting HIV protease cleavage sites in protein. J. Comput. Chem., 2002, 23, 267-274.
239. Liang, G.Z.; Li, S.Z. A new sequence representation as applied in better specificity elucidation for human immunodeficiency virus type 1 protease. Biopolymers, 2007, 88, 401-412.
240. Nanni, L.; Lumini, A. Using ensemble of classifiers for predicting HIV protease cleavage sites in proteins. Amino Acids, 2008, 36, 409-16.
241. Shen, H.B.; Chou, K.C. HIVcleave: a web-server for predicting HIV protease cleavage sites in proteins. Anal. Biochem., 2008, 375, 388-390.
242. Du, Q.S.; Wang, S.Q.; Wei, D.Q.; Zhu, Y.; Guo, H.; Sirois, S.; Chou, K.C. polyprotein cleavage mechanism of SARS CoV mpro and chemical modification of octapeptide. Peptides, 2004, 25, 1857-1864.
243. Du, Q.S.; Sun, H.; Chou, K.C. Inhibitor design for SARS coronavirus main protease based on "distorted key theory". Med. Chem., 2007, 3, 1-6.
244. Gan, Y.R.; Huang, H.; Huang, Y.D.; Rao, C.M.; Zhao, Y.; Liu, J.S.; Wu, L.; Wei, D.Q. Synthesis and activity of an octapeptide inhibitor designed for SARS coronavirus main proteinase. Peptides, 2006, 27, 622-625.
245. Nielsen, H.; Brunak, S.; von Heijne, G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng., 1999, 12, 3-9.
246. Chou, K.C. Prediction of protein signal sequences and their cleavage sites. Proteins: Struct., Funct., Genet., 2001, 42, 136-139.
247. Chou, K.C. Using subsite coupling to predict signal peptides. Protein Eng., 2001, 14, 75-79.
248. Bendtsen, J.D.; Nielsen, H.; von Heijne, G.; Brunak, S. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 2004, 340, 783-795.
249. Chou, K.C. Prediction of signal peptides using scaled window. Peptides, 2001, 22, 1973-1979.
250. Liu, H.; Yang, J.; Ling, J.G.; Chou, K.C. Prediction of protein signal sequences and their cleavage sites by statistical rulers. Biochem. Biophys. Res. Comm. (BBRC), 2005, 338, 1005-1011.
251. Hiss, J.A.; Schneider, G. Architecture, function and prediction of long signal peptides. Briefings Bioinformatics, 2009, 10, 569-578.
252. Shen, H.B.; Chou, K.C. Signal-3L: a 3-layer approach for predicting signal peptide. Biochem. Biophys. Res. Comm. (BBRC), 2007, 363, 297-303.
253. Xu, Y.; Shao, X.J.; Wu, L.Y.; Deng, N.Y.; Chou, K.C. iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins. PeerJ, 2013, 1, e171.
254. Xu, Y.; Wen, X.; Shao, X.J.; Deng, N.Y.; Chou, K.C. iHyd-PseAAC: Predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propensity into pseudo amino acid composition. Int. J. Mol. Sci., 2014, 15, 7594-7610.
255. Qiu, W.R.; Xiao, X.; Lin, W.Z.; Chou, K.C. iMethyl-PseAAC: Identification of protein methylation sites via a pseudo amino acid composition approach. Biomed. Re.s Int., 2014, 2014, 947416.
256. Xu, Y.; Wen, X.; Wen, L.S.; Wu, L.Y.; Deng, N.Y.; Chou, K.C. iNitro-Tyr: Prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition. PLoS One, 2014, 9, e105018.
257. Qiu, W.R.; Xiao, X.; Lin, W.Z.; Chou, K.C. iUbiq-Lys: Prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a grey system model Journal of Bio-molecular Structure and Dynamics (JBSD) 2014, doi:10.1080/07391102.2014.968875.
258. Liu, Z.; Xiao, X.; Qiu, W.R.; Chou, K.C. iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition. Anal. Biochem., 2015, doi:org/10.1016/j.ab.2014.1012.1009.
259. Chou, K.C.; Shen, H.B. A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0 PLoS ONE, 2010, 5, e9931.
260. Chou, K.C.; Shen, H.B. Plant-mPLoc: A Top-Down strategy to augment the power for predicting plant protein subcellular localization. PLoS One, 2010, 5, e11335.
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