Click2Drug-一个综合性的CADD网站

前言

在进行CADD相关操作时，我们一般都会去寻找相关的文献，软件，看看实现条件怎么样。

今天介绍一个网站，就是工具包的集合目录。

Directory of computer-aided Drug Design tools

web:https://click2drug.org

这个网站包含了CADD相关的各个方面：web，软件，网页等等。

虽然不是最新的，但还是比较齐全的。

涵盖了CADD相关的各个方面。

示例

挑选几个看一下。

1.药物相关的数据库

从ZINC到DUD-E还有很多，基本都包含了

2.结构展示

• UCSF Chimera. Open source, highly extensible program for interactive visualization and analysis of molecular structures and related data. Free of charge for academic, government, non-profit, and personal use. For Windows, Mac and Linux. Developed by the Resource for Biocomputing, Visualization, and Informatics, UCSF.
• Pymol. Open source, user-sponsored, molecular visualization system written in Python. Distributed by DeLano Scientific LLC. For Windows, Mac and Linux.
• OpenStructure. Open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics. Provided by the Swiss Institute of Bioinformatics and the Biozentrum, University of Basel.
• Swiss-PDB Viewer / DeepView. Program for 3D visualization of macromolecules, allowing to analyze several proteins at the same time. Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB).

3.分子模拟工具

• CHARMM. (Chemistry at HARvard Macromolecular Mechanics). Package of molecular simulation programs, including source code and demos.
• GROMACS. (GROningen MAchine for Chemical Simulations). Free open source molecular dynamics simulation package.
• Amber. (Assisted Model Building with Energy Refinement). Package of molecular simulation programs, including source code and demos.
• AmberTools. AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. It contains NAB (build molecules; run MD or distance geometry, using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models), antechamber and MCPB (create force fields for general organic molecules and metal centers), tleap and sleap (Basic preparation program for Amber simulations), sqm (semiempirical and DFTB quantum chemistry program), pbsa (Performs numerical solutions to Poisson-Boltzmann models), 3D-RISM (Solves integral equation models for solvation), ptraj and cpptraj (structure and dynamics analysis of trajectories), MMPBSA.py and amberlite (Energy-based analyses of MD trajectories)
• GROMACS. High performance toolkit for CPU/GPU-accelerated molecular dynamics simulation and setup. Can be used as a library or as an application with an intuitive Python interface. Developed, maintained and provided open-source by Standford University, United States.

4.分子对接

• Autodock. Free open source EA based docking software. Flexible ligand. Flexible protein side chains. Maintained by the Molecular Graphics Laboratory, The Scripps Research Institute, la Jolla.
• DOCK. Anchor-and-Grow based docking program. Free for academic usage. Flexible ligand. Flexible protein. Maintained by the Soichet group at the UCSF.
• GOLD. GA based docking program. Flexible ligand. Partial flexibility for protein. Product from a collaboration between the university of Sheffield, GlaxoSmithKline plc and CCDC.
• Glide. Exhaustive search based docking program. Exists in extra precision (XP), standard precision (SP) and virtual High Throughput Screening modes. Ligand and protein flexible. Provided by Schrödinger.
• Itzamna. Itzamna is a docking program, identifying active compounds for a given target. You can upload a protein and a docking is performed, either against an in-house database containing more than a million active compounds, or against a user-defined library. Provided by Mind The Byte.