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分子动力学：
| Amber20 | DS | AutoDock Vina | CHARMM | GROMACS | GROMOS | PyMol |
相似性搜索：
| SuperPred | SEA |
SuperPred， SEA搜索二维结构的相似性。可作为靶标预测的方法。
分子描述符与分子指纹计算工具：
PaDEL-descriptor是新加坡国立的Chun Wei Yap教授开发的分子描述符计算软件.Chun Wei Yap开发了一系列生物化学信息相关的程序PaDEL系列,这是其中分子描述符计算的程序. 程序是基于JAVA的,并提供了源代码.整合了很多的分子描述符,现在包括1875(1444个1D&2D描述符和431个3D描述符)个描述符以及12种分子指纹,并且有图形界面,输出为csv表格.
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在QSAR/SAR、虚拟筛选、数据库搜索、排名、药物ADME/T预测等药物发现过程中，小分子的分子表征已被广泛应用。为了促进对药物分子的广泛研究，我们开发了一个免费的、开源的python包，称为python中的化学信息学（ChemoPy），用于计算常用的结构和物理化学特征。它计算了16个药物特征组，由19个描述符组成，包括1135个描述符值。此外，它还提供了七种药物分子的分子指纹系统，包括拓扑指纹、电子拓扑状态（E-state）指纹、MACCS密钥、FP4密钥、原子对指纹、拓扑扭转指纹和Morgan/circular指纹。通过应用半经验量子化学程序MOPAC，ChemoPy还可以方便地计算出大量的三维分子描述符。
Molecular representation for small molecules has been routinely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes. To facilitate extensive studies of drug molecules, we developed a freely available, open-source python package called chemoinformatics in python (ChemoPy) for calculating the commonly used structural and physicochemical features. It computes 16 drug feature groups composed of 19 descriptors that include 1135 descriptor values. In addition, it provides seven types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pairs fingerprints, topological torsion fingerprints and Morgan/circular fingerprints. By applying a semi-empirical quantum chemistry program MOPAC, ChemoPy can also compute a large number of 3D molecular descriptors conveniently.
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经典定量结构-活性/性质关系（QSAR/QSPR）建模的一个关键步骤是将化合物编码成一个数值描述符向量。虽然大多数可用的化学信息学软件包提供了计算描述符的例程，但在大多数情况下并不容易使用。这个简单的命令行工具使用CDK和JOELib2将MDL-SD文件转换为ARFF和LIBSVM格式，用于机器学习和数据挖掘。
A key step in classical quantitative structure-activity/property relationship (QSAR/QSPR) modeling is the encoding of a chemical compound into a vector of numerical descriptors. Although most of the available chemoinformatic software packages provide routines for the calculation of descriptors they are not easy to use in most cases. This simple command-line tool converts an MDL SD file into ARFF and LIBSVM format for machine learning and data mining purposes using CDK and JOELib2.
蛋白质同源建模工具：
MODELLER用于蛋白质三维结构的同源或比较建模。用户可根据模型自动计算出一个包含所有非氢原子排列的模型。MODELLER通过满足空间约束（3,4）实现比较蛋白质结构建模，并可以执行许多附加任务，包括蛋白质结构环的从头建模、根据灵活定义的目标函数优化各种蛋白质结构模型、蛋白质序列的多重排列和/或结构、聚类、序列数据库搜索、蛋白质结构比较等。MODELLER可用于大多数Unix/Linux系统、Windows和Mac上下载。
MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download for most Unix/Linux systems, Windows, and Mac.
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2. SWISS-MODEL
SWISS-MODEL是一个完全自动化的蛋白质结构同源建模服务器，可通过ExPASy web服务器或从程序DeepView（瑞士Pdb查看器）访问。这个服务器的目的是让全世界所有生命科学研究人员都能访问蛋白质模型。
SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make protein modelling accessible to all life science researchers worldwide.
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药物重定位知识图谱 Drug Repurposing Knowledge Graph (DRKG)
- 下载 DRKG 知识图谱，DRKG 知识图谱已开源：https://dgl-data.s3-us-west-2.amazonaws.com/dataset/DRKG/drkg.tar.gz
探索「老药新用」最短路径：亚马逊AI Lab开源大规模药物重定位知识图谱DRKG
亚马逊AI Lab开源大规模药物重定位知识图谱DRKG (重要)
案例链接：
https://github.com/gnn4dr/DRKG/blob/master/embedding_analysis/Train_embeddings.ipynb
https://github.com/gnn4dr/DRKG/blob/master/drug_repurpose/COVID-19_drug_repurposing.ipynb
完整案例可以在此处获取：
https://github.com/gnn4dr/DRKG/blob/master/drug_repurpose/COVID-19_drug_repurposing.ipynb
分子文件格式转化工具：Babel，OpenBabel 图形显示工具：Chimera，Vida，ICM browser，DeepView，Rasmol，VMD =============== ============ ProBiS: a web server for detection of structurally similar protein binding sites (Nucleic Acids Res. 2010) ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment (Bioinformatics. 2010 ) =========== =========== ===============
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