# BioMedR # #介绍BioMedR包提供了一个R / Bioconductor包生成各种分子表示化学物质,蛋白质、dna / rna和他们的相互作用。看到的插曲(“BioMedR”)的全面的用户指南。# #安装安装BioMedR包R,只需输入源(“//www.anjoumacpherson.com/biocLite.R”) biocLite (BioMedR) BioMedR包全功能(特别是开放巴贝尔相关功能),我们建议用户安装_Enhances_包通过使用:源(“//www.anjoumacpherson.com/biocLite.R”) biocLite (Rcpi,依赖= c(“进口”,“增强”))几个BioMedR包的依赖关系,可能需要一些系统级图书馆,检查这些包的相应的手册详细的安装指南。# # Rcpi功能实现和集成先进的蛋白质序列描述符和分子描述符/指纹与r .蛋白质序列,Rcpi包可以*计算6个蛋白质描述符团体组成的14种常用的结构和物理化学描述符包括9920描述符。*计算广义范围的6种类型描述符中由不同的降维方法proteochemometric (PCM)建模。* Parallellized成对相似性计算导出了蛋白质序列比对和基因本体论(去)语义相似性度量列表内的蛋白质。小分子,Rcpi包* 307(计算分子描述符(2 d / 3 d),包括宪法、拓扑,几何,和电子描述符,等。*计算十多个类型的分子指纹,包括FP4钥匙,E-state指纹,MACCS钥匙,等,和并行化化学相似性搜索。*计算三个核酸成分特征描述当地的序列信息通过kmers (DNA序列的子序列)。*计算六个自相关特性描述的水平之间的相关性两个寡核苷酸沿着DNA序列的特定的物理化学性质。*计算两个伪核苷酸组成特性,可用于表示一个DNA序列离散模型或向量序列仍保持相当大的订单信息,特别是全球或远程订单信息序列,通过其组成寡核苷酸的物理化学性质。 * Parallelized pairwise similarity computation derived by fingerprints and maximum common substructure search within a list of small molecules. By combining various types of descriptors for drugs, proteins and DNA/RNA in different methods, interaction descriptors representing protein-protein, compound-compound, DNA-DNA, compound-DNA compound-protein and DNA-protein interactions could be conveniently generated withBioMedR, including: * Two types of compound-protein interaction (CPI) descriptors * Two types of compound-DNA interaction (CDI) descriptors * Two types of DNA-protein interaction (DPI) descriptors * Three types of protein-protein interaction (PPI) descriptors * Three types of compound-compound interaction (CCI) descriptors * Three types of DNA-DNA interaction (DDI) descriptors Several useful auxiliary utilities are also shipped with BioMedR: * Parallelized molecule and protein sequence retrieval from several online databases, like PubChem, ChEMBL, KEGG, DrugBank, UniProt, RCSB PDB, genBank, etc. * Loading molecules stored in SMILES/SDF files and loading protein sequences from FASTA/PDB files * Molecular file format conversion The computed protein sequence descriptors, molecular descriptors/fingerprints, interaction descriptors and pairwise similarities are widely used in various research fields relevant to drug disvery, primarily bioinformatics, chemoinformatics, proteochemometrics and chemogenomics. ## Links * Bioconductor Page: //www.anjoumacpherson.com/packages/release/bioc/html/BioMedR.html * Track Devel: https://github.com/wind22zhu/BioMedR * Report Bugs: https://github.com/wind22zhu/BioMedR/issues ## Contact The BioMedR package is developed by Computational Biology and Drug Design Group, Central South University, China. * Minfeng Zhu *东杰 曹*东升