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EpitopeVec: Linear Epitope Prediction Using Deep Protein Sequence Embeddings [article]

Akash Bahai, Ehsaneddin Asgari, Mohammad Mofrad, Andreas Kloetgen, Alice Carolyn McHardy
<span title="2020-11-26">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Results: We describe a new method called EpitopeVec, which utilizes residue properties, modified antigenicity scales, and a Protvec representation of peptides for linear BCE prediction with machine learning  ...  Availablity: The software is available at https://github.com/hzi-bifo/epitope-prediction under the GPL3.0 license  ...  to use machine learning for linear epitope prediction.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.26.395830">doi:10.1101/2020.11.26.395830</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lrd3a2hbvbfzpg2l352qf34fmi">fatcat:lrd3a2hbvbfzpg2l352qf34fmi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429104405/https://www.biorxiv.org/content/biorxiv/early/2020/11/26/2020.11.26.395830.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f7/9f/f79f32d5cf0b1caffc5a4fc88c36aab5bd95a472.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.26.395830"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

EpitopeVec: Linear Epitope Prediction Using Deep Protein Sequence Embeddings

Akash Bahai, Ehsaneddin Asgari, Mohammad R K Mofrad, Andreas Kloetgen, Alice C McHardy
<span title="2021-06-28">2021</span> <i title="Oxford University Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
We describe a new method called EpitopeVec, which uses a combination of residue properties, modified antigenicity scales, and protein language model-based representations (protein vectors) as features  ...  of peptides for linear BCE predictions.  ...  Notably, EpiDope, a recently published study, also makes use of protein embeddings, but it uses context-aware embeddings for each residue in the sequence by using a vector with a length of 1000, whereas  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btab467">doi:10.1093/bioinformatics/btab467</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34180989">pmid:34180989</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8652027/">pmcid:PMC8652027</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rl24qzn7c5ejjfdgrqy75qajcy">fatcat:rl24qzn7c5ejjfdgrqy75qajcy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210630033204/https://watermark.silverchair.com/btab467.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAv8wggL7BgkqhkiG9w0BBwagggLsMIIC6AIBADCCAuEGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMGuts1mIzsDtYlBv7AgEQgIICsogDvLLIHcmBpyRL5GbZb7bwawLBhUXuZUUP5P_N6gyzZCbFcCBlwVqIeN0y1or9bTiEoF1qfJxFOXm2U--mjGJsAu0j5pys9AJYqYJdwWiIzk9QDWY4PjL9mtSRPE7KQk0awwm-rDwX5xuFSSQ1uYuUcLJHzboA4JcpJw7PT0plu9fU4x7B2a0oyOlqosZ3KhmB2lPRY6-LO6vr9XTxZWaHYBGxKO9Oixlm3kCT_dHRrAHIDgNcrsMm3JZM3OB-lJLZhYbTWTIIlqJ3xNx_Q-2BD88R19bBqcbFuG_lPiPWIN5JYbgkSKAonIFL1MWW2B6eU3ALRub1-hNi28kIjcYl9xS54dGZc6e8pY9M2kinK593bhyvrvpaVg4zr-7Yo_CMnrSDVDduvqjjP990VYFaPt-qbqRlSdj_BFXrNlNClaiUGoM5Eo38WyxQt8lHkhKa3_49JAOKPbVbME_VFc_uIJ7qdW92zUrkYeX0ywHaW-W_6M8UpesTXVC29bvMgDsybDVoLfj6QC9d0kz990rYU7lYTzolHkPG_OwCrdfMGDBJAiorA6EbiJqm7aLu8vAXDzVAy2N34sj1_R_kcsv8rfwI_dd2jealfT6wpk2pKeXdidREhqC3K5PX0BpXZKLw2AQ6TGTbBBpvt9u-XU6ufnb7c93rFp9HYzKRIxQ6TAx0Av44ouqpfoOVXSNAtN1iimlMh7y7Wu8FQuMqRkq6FZguMIaJ27C6xyUcmaa8CGgv8rv1wOoSUt52IJtSQGpEu-PLU7wgBhb_9li6zptDSkNHyat1B4b2HLSoYvn1fn1Y2IbbhtR3Sb59X8EuGKVA3y3K6Cu-RQ1Ksm2cwvdGyX7HhIiC2Np8jeQt_Rl6VIzcRBpCl3S-HEP2Z3TA5lC4jDMxbw-qH-HZbcqMAs0cbA" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d9/7d/d97d3fd1364ea88a8b11e4e095306f7387c3a472.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btab467"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8652027" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>