@quantaosun
药企研发人员 / 在读博士 / 有机合成 / 分子模拟
Smina docking of a small molecule to a protein, then the top 3 poses evaluated by molecular dynamics to select out the best one.
Millions of small molecules will be downloaded from the ZINC database in 3D SDF file format, serving for docking based virtual screening purposes. Most of these molecules could be purchased.
7SI9 是新上市药物辉瑞新冠病毒特效药的常温下的晶体结构。这个项目尝试使用Gromacs对该结构进行绝对结合自由能（ABFE）计算，以希望得到一个结合自由能的数值与实验值进行比对。
7SI9 是新上市药物辉瑞新冠病毒特效药的常温下的晶体结构。这个项目尝试使用Gromacs对该结构进行绝对结合自由能（ABFE）计算，以希望得到一个结合自由能的数值与实验值进行比对。
Utilize the Make it rain/protein_ligand to generate SYS_gaff2.crd and SYS_gaff2.prctop file, then use as input for the waterswap notebook to do a 100 iteration for an estamate binding free energy.
您可能经常发现自己处于获得大量 2D 结构甚至只是一些Smiles字符串的情况。我们如何将这些重要的结构信息转换为 3D 结构，以便更多地关注像 QSAR 构建这样的实际任务？
基于元动力学的 ensemble docking 1. 普通动力学 2. 元动力学 3. 普通动力学ensemble docking 4. 元动力学 ensemble docking 5. 比较 6. 最终结果是使用空载apo靶点实现了holo负载靶点的一个类似诱导契合对接的过程。
Starting from a PDB bank structure or a local PDB structure, setting up and run a molecular dynamics simulation with user-friendly in mind, with Ambertools and OpenMM, by mostly clicking the mouse
Starting from a PDB bank structure or a local PDB structure, setting up and run a molecular dynamics simulation with user-friendly in mind, with Ambertools and OpenMM, by mostly clicking the mouse
Build a QSAR model for SARS-COV-2 with public data or your local data, The model molecular descriptors as independent variable, bioactivity as dependent variable, random forest as amathematical model.
This is a public repository from Github https://github.com/bioexcel/biobb_wf_virtual-screening . It provides a docking engine for virtual screening.
A QSAR model with public data or your local data, The model utilises molecular descriptors as the independent variable, bioactivity as the dependent variable, random forest as a mathematical model
Prepare a molecular dynamic simulation from scratch without installing local VMD, use LigParGen for topology, it is one of the most reliable MD for a general solution protein-ligand simulation.
Calculate the binding free energy difference between two small molecules against the same protein target. This is one has cost me quite some time, also one of my favorate repositories.
