PROSES: A Web Server for Sequence-Based Protein Encoding

被引:3
作者
Kosesoy, Irfan [1 ]
Gok, Murat [1 ]
Oz, Cemil [2 ]
机构
[1] Yalova Univ, Dept Comp Engn, TR-77100 Merkez, Yalova, Turkey
[2] Sakarya Univ, Dept Comp & Informat Sci, Sakarya, Turkey
关键词
feature extraction; machine learning; protein encoding; protein-protein interactions; AMINO-ACID-SEQUENCE; PHYSICOCHEMICAL FEATURES; PREDICTION; CLASSIFICATION; PEPTIDES; PROFEAT;
D O I
10.1089/cmb.2018.0049
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Recently, the number of the amino acid sequences shared in online databases is growing rapidly in huge amounts. By using sequence-derived features, machine learning algorithms are successfully applied to prediction of protein functional classes, protein-protein interactions, subcellular location, and peptides of specific properties in many studies. Protein Sequence Encoding System (PROSES) is a web server designed as freely and easily accessible for all researchers who want to use computational methods on protein sequence data. That is, PROSES provides users to encode their protein sequences easily without writing any programming code.
引用
收藏
页码:1120 / 1122
页数:3
相关论文
共 14 条
[1]   Classification of nuclear receptors based on amino acid composition and dipeptide composition [J].
Bhasin, M ;
Raghava, GPS .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2004, 279 (22) :23262-23266
[2]   Prediction of linear B-cell epitopes using amino acid pair antigenicity scale [J].
Chen, J. ;
Liu, H. ;
Yang, J. ;
Chou, K.-C. .
AMINO ACIDS, 2007, 33 (03) :423-428
[3]   PREDICTION OF PROTEIN-FOLDING CLASS USING GLOBAL DESCRIPTION OF AMINO-ACID-SEQUENCE [J].
DUBCHAK, I ;
MUCHNIK, I ;
HOLBROOK, SR ;
KIM, SH .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1995, 92 (19) :8700-8704
[4]   iFrag: A Protein-Protein Interface Prediction Server Based on Sequence Fragments [J].
Garcia-Garcia, Javier ;
Valls-Comamala, Victoria ;
Guney, Emre ;
Andreu, David ;
Munoz, Francisco J. ;
Fernandez-Fuentes, Narcis ;
Oliva, Baldo .
JOURNAL OF MOLECULAR BIOLOGY, 2017, 429 (03) :382-389
[5]   A new feature encoding scheme for HIV-1 protease cleavage site prediction [J].
Gok, Murat ;
Ozcerit, Ahmet Turan .
NEURAL COMPUTING & APPLICATIONS, 2013, 22 (7-8) :1757-1761
[6]  
Guo J., 2000, P 3 AS PAC BIOINF C, p[17, 117]
[7]   PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence [J].
Li, Z. R. ;
Lin, H. H. ;
Han, L. Y. ;
Jiang, L. ;
Chen, X. ;
Chen, Y. Z. .
NUCLEIC ACIDS RESEARCH, 2006, 34 :W32-W37
[8]  
Maetschke S, 2005, P 3 AS PAC BIOINF C, P141
[9]   Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence [J].
Rao, H. B. ;
Zhu, F. ;
Yang, G. B. ;
Li, Z. R. ;
Chen, Y. Z. .
NUCLEIC ACIDS RESEARCH, 2011, 39 :W385-W390
[10]   Highly accurate and consistent method for prediction of helix and strand content from primary protein sequences [J].
Ruan, JS ;
Wang, K ;
Yang, J ;
Kurgan, LA ;
Cios, K .
ARTIFICIAL INTELLIGENCE IN MEDICINE, 2005, 35 (1-2) :19-35