Molecular Cavity Topological Representation for Pattern Analysis: A NLP Analogy-Based Word2Vec Method

Dongliang Guo, Qiaoqiao Wang, Meng Liang, Wei Liu, Junlan Nie
<span title="2019-11-29">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
Cavity analysis in molecular dynamics is important for understanding molecular function. However, analyzing the dynamic pattern of molecular cavities remains a difficult task. In this paper, we propose a novel method to topologically represent molecular cavities by vectorization. First, a characterization of cavities is established through Word2Vec model, based on an analogy between the cavities and natural language processing (NLP) terms. Then, we use some techniques such as dimension
more &raquo; ... and clustering to conduct an exploratory analysis of the vectorized molecular cavity. On a real data set, we demonstrate that our approach is applicable to maintain the topological characteristics of the cavity and can find the change patterns from a large number of cavities.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms20236019">doi:10.3390/ijms20236019</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31795343">pmid:31795343</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6928730/">pmcid:PMC6928730</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vxme5vblcrbm7g5en3dh25t7ly">fatcat:vxme5vblcrbm7g5en3dh25t7ly</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191208005359/https://res.mdpi.com/d_attachment/ijms/ijms-20-06019/article_deploy/ijms-20-06019.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/ce/fe/cefeb1b7c6c547e66255fc5b543f9617cd111593.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms20236019"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6928730" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>