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Leveraging family-specific signatures for AMP discovery and high-throughput annotation.

Waghu FH, Barai RS, Idicula-Thomas S - Sci Rep (2016)

Bottom Line: As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance.The webserver is available online at www.campsign.bicnirrh.res.in.In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India.

ABSTRACT
Antimicrobial peptides (AMPs) are diverse, biologically active, essential components of the innate immune system. As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance. They are widely researched for their therapeutic potential, especially against multi-drug resistant pathogens. AMPs are known to have family-specific sequence composition, which can be mined for their discovery and rational design. Here, we present a detailed family-based study on AMP families. The study involved the use of sequence signatures represented by patterns and hidden Markov models (HMMs) present in experimentally studied AMPs to identify novel AMPs. Along with AMPs, peptides hitherto lacking antimicrobial annotation were also retrieved and wet-lab studies on randomly selected sequences proved their antimicrobial activity against Escherichia coli. CAMPSign, a webserver has been created for researchers to effortlessly exploit the use of AMP family signatures for identification of AMPs. The webserver is available online at www.campsign.bicnirrh.res.in. In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.

No MeSH data available.


Related in: MedlinePlus

Flowchart of (a) design and (b) working of CAMPSign webserver.
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f4: Flowchart of (a) design and (b) working of CAMPSign webserver.

Mentions: The performance of the tool was measured in terms of recall/sensitivity, specificity, precision/ positive predictive value (PPV) and negative predictive value (NPV). Specificity is the probability of a non-AMP being correctly predicted as non-antimicrobial. NPV is the ratio of non-AMPs (true negatives) and all predicted non-AMPs. All values have been calculated as percentage. Flow chart of the design and working of CAMPSign can be seen in Fig. 4.


Leveraging family-specific signatures for AMP discovery and high-throughput annotation.

Waghu FH, Barai RS, Idicula-Thomas S - Sci Rep (2016)

Flowchart of (a) design and (b) working of CAMPSign webserver.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836297&req=5

f4: Flowchart of (a) design and (b) working of CAMPSign webserver.
Mentions: The performance of the tool was measured in terms of recall/sensitivity, specificity, precision/ positive predictive value (PPV) and negative predictive value (NPV). Specificity is the probability of a non-AMP being correctly predicted as non-antimicrobial. NPV is the ratio of non-AMPs (true negatives) and all predicted non-AMPs. All values have been calculated as percentage. Flow chart of the design and working of CAMPSign can be seen in Fig. 4.

Bottom Line: As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance.The webserver is available online at www.campsign.bicnirrh.res.in.In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India.

ABSTRACT
Antimicrobial peptides (AMPs) are diverse, biologically active, essential components of the innate immune system. As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance. They are widely researched for their therapeutic potential, especially against multi-drug resistant pathogens. AMPs are known to have family-specific sequence composition, which can be mined for their discovery and rational design. Here, we present a detailed family-based study on AMP families. The study involved the use of sequence signatures represented by patterns and hidden Markov models (HMMs) present in experimentally studied AMPs to identify novel AMPs. Along with AMPs, peptides hitherto lacking antimicrobial annotation were also retrieved and wet-lab studies on randomly selected sequences proved their antimicrobial activity against Escherichia coli. CAMPSign, a webserver has been created for researchers to effortlessly exploit the use of AMP family signatures for identification of AMPs. The webserver is available online at www.campsign.bicnirrh.res.in. In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.

No MeSH data available.


Related in: MedlinePlus