Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India.
Curr Drug Targets. 2019;20(5):501-521. doi: 10.2174/1389450119666181022153016.
Molecular docking is a process through which small molecules are docked into the macromolecular structures for scoring its complementary values at the binding sites. It is a vibrant research area with dynamic utility in structure-based drug-designing, lead optimization, biochemical pathway and for drug designing being the most attractive tools. Two pillars for a successful docking experiment are correct pose and affinity prediction. Each program has its own advantages and drawbacks with respect to their docking accuracy, ranking accuracy and time consumption so a general conclusion cannot be drawn. Moreover, users don't always consider sufficient diversity in their test sets which results in certain programs to outperform others. In this review, the prime focus has been laid on the challenges of docking and troubleshooters in existing programs, underlying algorithmic background of docking, preferences regarding the use of docking programs for best results illustrated with examples, comparison of performance for existing tools and algorithms, state of art in docking, recent trends of diseases and current drug industries, evidence from clinical trials and post-marketing surveillance are discussed. These aspects of the molecular drug designing paradigm are quite controversial and challenging and this review would be an asset to the bioinformatics and drug designing communities.
分子对接是一种将小分子对接到大分子结构中的过程，以对结合位点的互补值进行评分。它是一个充满活力的研究领域，在基于结构的药物设计、先导化合物优化、生化途径和药物设计中具有动态效用，是最有吸引力的工具。成功进行对接实验的两个关键是正确的构象和亲和力预测。每个程序在对接准确性、排序准确性和时间消耗方面都有自己的优势和缺点，因此不能得出一般性结论。此外，用户在测试集中并不总是考虑足够的多样性，这导致某些程序的表现优于其他程序。在这篇综述中，主要关注对接的挑战和现有程序中的故障排除、对接的基本算法背景、使用对接程序获得最佳结果的偏好（举例说明）、现有工具和算法的性能比较、对接的最新进展、疾病和当前药物工业的趋势、临床试验和上市后监测的证据。分子药物设计范例的这些方面非常有争议和具有挑战性，本综述将成为生物信息学和药物设计社区的宝贵资源。
