Laboratory of Computational Modeling of Drugs, South Ural State University, Pr. Lenina, 76, Chelyabinsk 454080, Russian Federation.
ITMO University, St. Petersburg 197101, Russian Federation.
Curr Top Med Chem. 2018;18(22):1955-1975. doi: 10.2174/1568026619666181129142127.
The review describes online resources used for drug discovery and design. Internet resources can be classified into two classes. The first class of resources accumulates information about drugs, drug candidates, compounds, and bioassays. This information is a starting point in drug discovery and design. It is necessary for a training dataset composition. The data found at this step are needed in the search for the rules predicting a biological activity or recognizing active compounds among other molecules. The following databases can be used: ChEMBL, different databases of US National Institutes of Health, DrugBank, PDBind-CN Database, RCSB Protein Data Bank (PDB), BRENDA, etc. The second class of Internet resources includes web-portals performing online computations for drug discovery and design. The web-portals perform: 1) modelling of molecular structure such as geometry optimization and molecular docking; 2) online computations of various descriptors, physical-chemical and ADMET properties influencing the bioprocesses occurring in a living organism along the road of the drug therapeutic action; 3) quantitative structure-activity relationship (QSAR) and quantitative structure-property relationship (QSPR) studies; 4) prognosis of bioactivities of compounds; 5) design of new drug candidates. These are, for example, ChemAxon, ACD/ I-lab, Mcule, OCHEM, eADMET, ChemoSophia, DockingServer, 1-click Docking, MDWeb, DockingServer, ZDOCK, etc. The role of docking online resources for modeling of "ligand-receptor" complexes, prognosis of bioactivities, and drug design is discussed. The review highlights the possibilities of Internet resources for a study of a drug action at the most important stages. A detailed assessment of the advantages of the reviewed Internet resources is done.
本文综述了用于药物发现和设计的在线资源。互联网资源可以分为两类。第一类资源积累了有关药物、药物候选物、化合物和生物测定的信息。这些信息是药物发现和设计的起点，也是组成训练数据集的必要条件。在寻找预测生物活性或识别其他分子中活性化合物的规则时，需要在这一步找到的数据。可以使用以下数据库：ChEMBL、美国国立卫生研究院的不同数据库、DrugBank、PDBind-CN 数据库、RCSB 蛋白质数据库 (PDB)、BRENDA 等。第二类互联网资源包括执行药物发现和设计在线计算的网络门户。这些网络门户执行：1) 分子结构建模，如几何优化和分子对接；2) 在线计算影响生物过程的各种描述符、物理化学和 ADMET 特性，这些生物过程沿着药物治疗作用的道路在生物体中发生；3) 定量构效关系 (QSAR) 和定量构效关系 (QSPR) 研究；4) 化合物生物活性的预测；5) 新药物候选物的设计。例如，ChemAxon、ACD/ I-lab、Mcule、OCHEM、eADMET、ChemoSophia、DockingServer、1-click Docking、MDWeb、DockingServer、ZDOCK 等。讨论了对接在线资源在建模“配体-受体”复合物、生物活性预测和药物设计中的作用。本文强调了互联网资源在药物作用的最重要阶段研究中的可能性。对所综述的互联网资源的优势进行了详细评估。
