Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

By H. Rao, Feng Zhu, G. Yang, Ze-Rong Li, Yu Zong Chen. Nucleic Acids Res., 2006

302 citations recorded by the source corpus.

Sequence-derived structural and physicochemical features have been extensively used for analyzing and predicting structural, functional, expression and interaction profiles of proteins and peptides. PROFEAT has been developed as a web server for computing commonly used features of proteins and peptides from amino acid sequence. To facilitate more extensive studies of protein and peptides, numerous improvements and updates have been made to PROFEAT. We added new functions for computing descriptors of protein–protein and protein–small molecule interactions, segment descriptors for local properties of protein sequences, topological descriptors for peptide sequences and small molecule structures. We also added new feature groups for proteins and peptides (pseudo-amino acid composition, amphiphilic pseudo-amino acid composition, total amino acid properties and atomic-level topological descriptors) as well as for small molecules (atomic-level topological descriptors). Overall, PROFEAT computes 11 feature groups of descriptors for proteins and peptides, and a feature group of more than 400 descriptors for small molecules plus the derived features for protein–protein and protein–small molecule interactions. Our computational algorithms have been extensively tested and used in a number of published works for predicting proteins of specific structural or functional classes, protein–protein interactions, peptides of specific functions and quantitative structure activity relationships of small molecules. PROFEAT is accessible free of charge at http://bidd.cz3.nus.edu.sg/cgi-bin/prof/protein/profnew.cgi.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d2ad7a1191aed6bfe435cb2d82d39612a391fce7

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In Molecular Biology

1. Aiping Lu
2. Ning-Ning Wang
3. Jie Dong
4. Zhi-Jiang Yao
5. Ming Wen
6. Minfeng Zhu
7. Wenbin Zeng
8. Dongsheng Cao

Citations in the corpus

• BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions (2016, methodology): “Several bioinformatics packages for computing structural and physicochemical features of proteins or DNAs/ RNAs have been previously developed, including PROFEAT [41], BioJava [42], PseAAC, propy [43], repDNA [44], repRNA [45], protr [46] etc.”
• A Systematic Prediction of Multiple Drug-Target Interactions from Chemical, Genomic, and Pharmacological Data (2012, background): “cgi), involving descriptors like Moran autocorrelation, Dipeptide composition and so on [24].”