Waghu Faiza Hanif, Barai Ram Shankar, Gurung Pratima, Idicula-Thomas Susan
Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India.
Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
Nucleic Acids Res. 2016 Jan 4;44(D1):D1094-7. doi: 10.1093/nar/gkv1051. Epub 2015 Oct 13.
Antimicrobial peptides (AMPs) are known to have family-specific sequence composition, which can be mined for discovery and design of AMPs. Here, we present CAMPR3; an update to the existing CAMP database available online at www.camp3.bicnirrh.res.in. It is a database of sequences, structures and family-specific signatures of prokaryotic and eukaryotic AMPs. Family-specific sequence signatures comprising of patterns and Hidden Markov Models were generated for 45 AMP families by analysing 1386 experimentally studied AMPs. These were further used to retrieve AMPs from online sequence databases. More than 4000 AMPs could be identified using these signatures. AMP family signatures provided in CAMPR3 can thus be used to accelerate and expand the discovery of AMPs. CAMPR3 presently holds 10247 sequences, 757 structures and 114 family-specific signatures of AMPs. Users can avail the sequence optimization algorithm for rational design of AMPs. The database integrated with tools for AMP sequence and structure analysis will be a valuable resource for family-based studies on AMPs.
抗菌肽（AMPs）具有家族特异性的序列组成，可用于挖掘以发现和设计抗菌肽。在此，我们展示了CAMPR3；它是对现有CAMP数据库（可在www.camp3.bicnirrh.res.in在线获取）的更新。它是一个包含原核和真核抗菌肽序列、结构及家族特异性特征的数据库。通过分析1386个经过实验研究的抗菌肽，为45个抗菌肽家族生成了由模式和隐马尔可夫模型组成的家族特异性序列特征。这些特征进一步用于从在线序列数据库中检索抗菌肽。使用这些特征可鉴定出4000多个抗菌肽。因此，CAMPR3中提供的抗菌肽家族特征可用于加速和扩展抗菌肽的发现。CAMPR3目前包含10247个序列、757个结构和114个抗菌肽家族特异性特征。用户可以利用序列优化算法进行抗菌肽的合理设计。该数据库与抗菌肽序列和结构分析工具集成，将成为基于家族的抗菌肽研究的宝贵资源。
