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Protocols

PROFEAT specifications

Information


Unique identifier OMICS_09957
Name PROFEAT
Alternative name Protein Features
Interface Web user interface
Restrictions to use None
Input data The sequence of a protein or a peptide, in single-letter code and RAW format, as well as FASTA format, can be input in a window provided.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Z.R. Li
  • person_outline W.P. Chen

Publications for Protein Features

PROFEAT citations

 (22)
library_books

Surveying alignment free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers

2018
BMC Bioinformatics
PMCID: 5934817
PMID: 29724166
DOI: 10.1186/s12859-018-2148-8

[…] easures for ortholog detection across characterized yeast proteomes representing benchmark datasets. These alignment-free protein features are listed below, and most of them (5–10) are defined in the PROFEAT-Protein Feature Server [] while four-color maps and Nandy’s descriptors (1–2) can be calculated by using our alignment-free graphical-numerical-encoding program [] available at https://sourcef […]

library_books

Drug target interaction prediction via class imbalance aware ensemble learning

2016
BMC Bioinformatics
PMCID: 5259867
PMID: 28155697
DOI: 10.1186/s12859-016-1377-y

[…] targets using common chemical functional groups and pseudo amino acid composition, respectively [], while Yu et al. used molecular descriptors that were calculated using the DRAGON package [] and the PROFEAT web server [] for drugs and targets, respectively []. Other descriptors have also been used such as position-specific scoring matrices [], 2D molecular fingerprints [], MACCS fingerprints [], […]

library_books

Applicability of predictive toxicology methods for monoclonal antibody therapeutics: status Quo and scope

2016
PMCID: 5364268
PMID: 27766364
DOI: 10.1007/s00204-016-1876-7

[…] arking would have to be incorporated to select relevant descriptor sets (van Westen et al. , ). Descriptor for proteins molecules can be generated by different software such as PseAAC, Protein Recon, PROFEAT and ProtDCal, of which ProtDCal, a freely available tool with a friendly graphical user interface, has the capacity to generate a higher number of non-redundant of molecular descriptors for pr […]

library_books

Roles of d Amino Acids on the Bioactivity of Host Defense Peptides

2016
Int J Mol Sci
PMCID: 4964399
PMID: 27376281
DOI: 10.3390/ijms17071023

[…] es [,]. In QSAR studies of peptides, z-scale descriptors [] are widely used but are unable to describe the d-AAs. Furthermore, more comprehensive softwares for computing molecular descriptors such as PROFEAT [] and protr [] also undergo the same problem as they too do not differentiate between the l and d isoform, which therefore poses a problem for studies investigating d-AA-containing peptides. […]

call_split

Systems Pharmacology Dissecting Holistic Medicine for Treatment of Complex Diseases: An Example Using Cardiocerebrovascular Diseases Treated by TCM

2015
PMCID: 4460250
PMID: 26101539
DOI: 10.1155/2015/980190
call_split See protocol

[…] characterize the interactions of drug and protein, drug structures and protein sequences were converted into numerical descriptors by employing DRAGON program (http://www.talete.mi.it/index.htm) and PROFEAT WEBSEVER (http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi/), respectively (see details in Table S3). The multiple DTIs were represented by concatenating these chemical and protein descriptors […]

library_books

ProtDCal: A program to compute general purpose numerical descriptors for sequences and 3D structures of proteins

2015
BMC Bioinformatics
PMCID: 4432771
PMID: 25982853
DOI: 10.1186/s12859-015-0586-0

[…] ting operators were applied separately, leading to six sub-datasets of 45494 descriptors each.Shannon entropy was used to assess the variability of the eight datasets of descriptors (six PROTCAL plus PROFEAT and PROTEIN RECON). Additional file provides the Shannon entropy rankings for the eight datasets. Figure  plots the number of descriptors (x-axis), in each dataset, with entropy values larger […]

Citations

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PROFEAT institution(s)
Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore; School of Medicine, Hangzhou Normal University, Hangzhou, China; Innovative Drug Research Centre and College of Chemistry and Chemical Engineering, Chongqing University, Chongqing, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China; College of Chemistry, Sichuan University, Chengdu, China; Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, China; Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University, Nanchang, China
PROFEAT funding source(s)
Supported by Singapore Academic Research Fund [R-148-000-208-112]; National Natural Science Foundation of China [81202459]; and Fundamental Research Funds for the Central Universities [CQDXWL-2012-Z003, CDJZR14-46-88-01].

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