Computer-Aided Molecular "Biosilico" Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Cumbayá, Quito , Ecuador.
Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades Médicas; and Instituto de Simulación Computacional (ISC-USFQ) , Universidad San Francisco de Quito (USFQ) , Diego de Robles y vía Interoceánica , Quito 170157 , Pichincha , Ecuador.
J Chem Inf Model. 2020 Feb 24;60(2):1042-1059. doi: 10.1021/acs.jcim.9b00629. Epub 2019 Oct 30.
This report introduces the software (acronym for lti-near ap based on -Metric and ntact atrices of 3D rotein and mino-acid weighting), designed to compute tensor-based 3D protein structural descriptors by applying two- and three-linear algebraic forms. Moreover, these descriptors contemplate generalizing components such as 3D protein structural representations, (dis)similarity metrics, and multimetrics to extract geometrical related information between two and three amino acids, weighting schemes based on amino acid properties, matrix normalization procedures that consider simple-stochastic and mutual probability transformations, topological and geometrical cutoffs, amino acid, and group-based MD calculations, and aggregation operators for merging amino acidic and group MDs. The MuLiMs-MCoMPAs software, which belongs to the ToMoCoMD-CAMPS suite, was developed in Java (version 1.8) using the Chemistry Development Kit (CDK) (version 1.4.19) and the Jmol libraries. This software implemented a divide-and-conquer strategy to parallelize the computation of the indices as well as modules for data preprocessing and batch computing functionalities. Furthermore, it consists of two components: (i) a desktop-graphical user interface (GUI) and (ii) an API library. The relevance of this novel approach is demonstrated through two analyses that considered Shannon's entropy-based variability and a principal component analysis. These studies showed that the MuLiMs-MCoMPAs' three-linear descriptor family contains higher informational entropy than several other descriptors generated with available computation tools. Moreover, the MuLiMs-MCoMPAs indices capture additional orthogonal information to the one codified by the available calculation approaches. As a result, two sets of suggested theoretical configurations that contain two-linear indices and three-linear indices are available for download at tomocomd.com . Furthermore, as a demonstration of the applicability and easy integration of the MuLiMs library into a QSAR-based expert system, a software application ( was generated to predict SCOP protein structural classes and folding rate. It can thus be anticipated that the MuLiMs-MCoMPAs framework will turn into a valuable contribution to the chem- and bioinformatics research fields.
本报告介绍了软件（基于张量的 lti-near ap 的缩写，基于 3D 蛋白质和氨基酸的度量和接触矩阵进行加权），旨在通过应用二维和三维线性代数形式来计算基于张量的 3D 蛋白质结构描述符。此外，这些描述符考虑将 3D 蛋白质结构表示、（不）相似性度量和多度量等组件推广到两个和三个氨基酸之间的几何相关信息，基于氨基酸性质的加权方案，考虑简单随机和相互概率变换、拓扑和几何截止值、氨基酸和基于组的 MD 计算的矩阵归一化过程，以及用于合并氨基酸和组 MD 的聚合运算符。MuLiMs-MCoMPAs 软件属于 ToMoCoMD-CAMPS 套件，使用 Java（版本 1.8）开发，使用 Chemistry Development Kit (CDK)（版本 1.4.19）和 Jmol 库。该软件实现了一种分而治之的策略，以并行化指数的计算以及数据预处理和批处理功能的模块。此外，它由两个组件组成：(i) 桌面图形用户界面 (GUI) 和 (ii) API 库。这种新方法的相关性通过两项分析得到证明，这些分析考虑了基于香农熵的变异性和主成分分析。这些研究表明，MuLiMs-MCoMPAs 的三线性描述符族比其他几个可用计算工具生成的描述符包含更高的信息熵。此外，MuLiMs-MCoMPAs 指数捕捉到了可用计算方法编码的信息之外的额外正交信息。因此，tomocomd.com 上提供了两套建议的理论配置，其中包含两个线性指数和三个线性指数。此外，作为 MuLiMs 库在基于 QSAR 的专家系统中的应用和易于集成的演示，生成了一个软件应用程序 ( 用于预测 SCOP 蛋白质结构类和折叠速率。因此，可以预期 MuLiMs-MCoMPAs 框架将成为化学和生物信息学研究领域的有价值贡献。
