Recent advances in predicting protein classification and their applications to drug development

Current Topics in Medicinal Chemistry

Volumn 13, Issue 14, 2013, Pages 1622-1635

  Xiao, Xuan ^a,b,d   Lin, Wei Zhong ^a   Chou, Kuo Chen ^c,d  

^a JINGDEZHEN CERAMIC INSTITUTE   (China)

^b Zhejiang Textile and Fashion College   (China)

^c KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

^d GORDON LIFE SCIENCE INSTITUTE   (United States)

Author keywords

Discrete model; DNA binding protein; GPCR type; Protein attribute predictor; Protein subcellular localization; PseAAC; Web servers

Indexed keywords

AMINO ACID; CELL NUCLEUS RECEPTOR; DNA BINDING PROTEIN; G PROTEIN COUPLED RECEPTOR; SECRETORY PROTEIN;

ALGORITHM; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; AUTOMATION; BINDING SITE; CELLULAR DISTRIBUTION; CLASSIFICATION; COMPUTER PROGRAM; DRUG DESIGN; HIGH THROUGHPUT SCREENING; MACHINE LEARNING; PREDICTION; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEOMICS; REDUNDANCY ANALYSIS; REVIEW;

ALGORITHMS; ANIMALS; BINDING SITES; DRUG DESIGN; HUMANS; MODELS, MOLECULAR; PHARMACEUTICAL PREPARATIONS; PROTEINS;

EID: 84887972825     PISSN: 15680266     EISSN: 18734294     Source Type: Journal    
DOI: 10.2174/15680266113139990113     Document Type: Review

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135. Lin, K.; Qian, Z. L.; Lu, L.; Lu, L. Y.; Lai, L. H.; Gu, J. Y.; Zeng, Z. B.; Li, H. P.; Cai, Y. D. Predicting miRNA's target from primary structure by the nearest neighbor algorithm. Mol Divers, 2010, 14, 719-729.
136. Wang, W.; Geng, X.; Dou, Y.; Liu, T.; Zheng, X. Predicting protein subcellular localization by pseudo amino acid composition with a segment-weighted and features-combined approach. Protein Pept Lett, 2011, 18, 480-487.
137. Xiong, Y.; Liu, J.; Wei, D. Q. An accurate feature-based method for identifying DNA-binding residues on protein surfaces. Proteins, 2011, 79, 509-517.
138. Xu, Q.; Pan, S. J.; Xue, H. H.; Yang, Q. Multitask learning for protein subcellular location prediction. IEEE/ACM Trans Comput Biol Bioinform, 2011, 8, 748-759.
139. Xiao, X.; Wang, P.; Chou, K. C. iNR-PhysChem: a sequencebased predictor for identifying nuclear receptors and their subfamilies via physical-chemical property matrix. PLoS ONE, 2012, 7, e30869.
140. Garg, P.; Sharma, V.; Chaudhari, P.; Roy, N. SubCellProt: predicting protein subcellular localization using machine learning approaches. In silico biology, 2009, 9, 35-44.
141. Lin, W. Z.; Xiao, X.; Chou, K. C. GPCR-GIA: a web-server for identifying G-protein coupled receptors and their families with grey incidence analysis. Protein Eng Des Sel, 2009, 22, 699-705.
142. Rogers, J.; Gunn, S. Identifying feature relevance using a random forest. Lect Notes Comput Sc, 2006, 3940, 173-184.
143. Breiman, L. Random forests. Mach Learn, 2001, 45, 5-32.
144. Breiman, L. Randomizing outputs to increase prediction accuracy. Mach Learn, 2000, 40, 229-242.
145. Nimrod, G.; Schushan, M.; Szilagyi, A.; Leslie, C.; Ben-Tal, N. iDBPs: a web server for the identification of DNA binding proteins. Bioinformatics, 2010, 26, 692-693.
146. Nimrod, G.; Szilagyi, A.; Leslie, C.; Ben-Tal, N. Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. J Mol Biol, 2009, 387, 1040-1053.
147. Pugalenthi, G.; Kandaswamy, K. K.; Chou, K. C.; Vivekanandan, S.; Kolatkar, P. RSARF: prediction of residue solvent accessibility from protein sequence using random forest method. Protein Pept Lett, 2012, 19, 50-56.
148. Cao, J. Z.; Liu, W. Q.; Gu, H. Predicting Viral Protein Subcellular Localization with Chou's Pseudo Amino Acid Composition and Imbalance-Weighted Multi-Label K-Nearest Neighbor Algorithm. Protein Pept Lett, 2012, 19, 1163-1169.
149. He, Z.; Zhang, J.; Shi, X. H.; Hu, L. L.; Kong, X.; Cai, Y. D.; Chou, K. C. Predicting drug-target interaction networks based on functional groups and biological features. PLoS ONE, 2010, 5, e9603.
150. Huang, T.; Chen, L.; Cai, Y. D.; Chou, K. C. Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property. PLoS ONE, 2011, 6, e25297.
151. Huang, T.; He, Z. S.; Cui, W. R.; Cai, Y. D.; Shi, X. H.; Hu, L. L.; Chou, K. C. A Sequence-based Approach for Predicting Protein Disordered Regions. Protein and Peptide Letters, 2013, 20, 243-248.
152. Huang, T.; Shi, X. H.; Wang, P.; He, Z.; Feng, K. Y.; Hu, L.; Kong, X.; Li, Y. X.; Cai, Y. D.; Chou, K. C. Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks PLoS ONE, 2010, 5, e10972.
153. Li, B. Q.; Hu, L. L.; Niu, S.; Cai, Y. D.; Chou, K. C. Predict and analyze S-nitrosylation modification sites with the mRMR and IFS approaches. Journal of Proteomics, 2012, 75, 1654-1665.
154. Li, B. Q.; Huang, T.; Liu, L.; Cai, Y. D.; Chou, K. C. Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network. PLoS ONE, 2012, 7, e33393.
155. Hu, L. L.; Chen, C.; Huang, T.; Cai, Y. D.; Chou, K. C. Predicting biological functions of compounds based on chemical-chemical interactions. PLoS ONE, 2011, 6, e29491.
156. Hu, L. L.; Huang, T.; Cai, Y. D.; Chou, K. C. Prediction of Body Fluids where Proteins are Secreted into Based on Protein Interaction Network. PLoS One, 2011, 6, e22989.
157. Huang, T.; Wang, J.; Cai, Y. D.; Yu, H.; Chou, K. C. Hepatitis C virus network based classification of hepatocellular cirrhosis and carcinoma. PLoS ONE, 2012, 7, e34460.
158. Chou, K. C.; Shen, H. B. Review: recent advances in developing web-servers for predicting protein attributes (doi: 10. 4236/ns. 2009. 12011). Natural Science, 2009, 2, 63-92 (openly accessible at http://www. scirp. org/journal/NS/).
159. Lin, S. X.; Lapointe, J. Theoretical and experimental biology in one-A symposium in honour of Professor Kuo-Chen Chou's 50th anniversary and Professor Richard Giegé's 40th anniversary of their scientific careers. J. Biomedical Science and Engineering (JBiSE), 2013, 6, 435-442 (open accessible at http://www. scirp. org/journal/jbise/, doi: 410. 4236/jbise. 2013. 64054).
160. Lin, W. Z.; Fang, J. A.; Xiao, X.; Chou, K. C. iLoc-Animal: A multi-label learning classifier for predicting subcellular localization of animal proteins Molecular BioSystems, 2013, 9, 634-644.
161. King, B. R.; Vural, S.; Pandey, S.; Barteau, A.; Guda, C. ngLOC: software and web server for predicting protein subcellular localization in prokaryotes and eukaryotes. BMC research notes, 2012, 5, 351.
162. Chen, Y. C.; Wright, J. D.; Lim, C. DR-bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry. Nucleic acids research, 2012, 40, W249-256.
163. Cheng, X.; Xiao, X.; Wu, Z. C.; Wang, P.; Lin, W. Z. Swfoldrate: Predicting protein folding rates from amino acid sequence with sliding window method. Proteins, 2013, 81, 140-148.
164. Wang, P.; Xiao, X.; Chou, K. C. NR-2L: a two-level predictor for identifying nuclear receptor subfamilies based on sequence-derived features. PLoS ONE, 2011, 6, e23505.
165. Chou, K. C.; Elrod, D. W. Bioinformatical analysis of G-proteincoupled receptors. Journal of Proteome Research, 2002, 1, 429-433.