Qute Sun

Quantao's personal site to share chemistry knowledge, you couldaccess to this website by quantaosun.github.io

A Chinese platform providing free GPU - Baidu AI Studio PadelPadel

A tutorial for Gromacs protein-ligand simulation on PadelPadel

Posted by Quantao on February 03, 2022

NAMD FEP with Feprepare web server and NAMD

An tutorial for FEP calculation with Maestro, Feprepare server and NAMD

Posted by Quantao on December 18, 2021

Cloud FEP on Google Colab with Academic Desmond

An ipython notebook for free FEP calculation with GPU on Colab

Posted by Quantao on July 20, 2021

Happy and Free Docking with AutoDock (Smina)

A free ipython notebook for docking and visualization

Posted by Quantao on July 8, 2021

NAMD job control script for Baidu AI Studio

A csh script converting to a bash script

Posted by Quantao on July 6, 2021

A python script for converting IC50 to pIC50

A python script for converting IC50 to pIC50

Posted by Quantao on June 16, 2021

Absolute Binding Free Energy Calculation by Gromacs on GPU cloud

A notebook for running GPU based Gromacs on google colab

Posted by Quantao on June 10, 2021

Pymol image making with local Jupyter notebook

A notebook for running ipymol

Posted by Quantao on May 12, 2021

NAMD simulation with GPU acceleration on AI studion.

A notebook for running a normal protein-ligand MD

Posted by Quantao on May 11, 2021

Absolute free energy calculation with Gromacs

Some shared file like run.sh are listed here.

Posted by Quantao on April 19, 2021

Diels-Alder reaction-things you need to know

The classical D-A reaction discussed in many aspects.

Posted by Quantao on February 08, 2021

Small molecule ligand relative affinity calculation.

Free energy input files set up by a web server

Posted by Quantao on January 11, 2021

FEP patch scripts

Two scripts that could improve the Feprepare were provided.

Posted by Quantao on January 10, 2021

Name Reaction Classificaion.

The book, Jie Jack Li name reactions was reorgnized by reation types, names and compounds names.

Posted by Quantao on December 31, 2020

Protein-ligand water solution simulation tutorial by Gromacs.

Crazy detailed steps listed for gromacs simulation of protein-ligand complex in water solution.

Posted by Quantao on December 29, 2020

Quick Gromacs Compilation

A dirty compilation and some de-bug process.

Posted by Quantao on December 25, 2020

Don't work hard, work smart

Knime to make your life easier when process tedious work.

Posted by Quantao on December 22, 2020

Gromacs installation, running and result analysis

This tutorial uses a pure protein without ligand to show how to do a basic molecular dynamic simulation quickly on your laptop.

Posted by Quantao on December 17, 2020

PyMOL tutorial to make image.

PyMOL is a widely used visualization tool for proteins, membranes, small molecules, sometime, a high-quality image worth more than a thousand words.

Posted by Quantao on December 14, 2020

Turn Positive to Negative

TMSCN as a masking group, can turn to the acyl group from "positive" to "negative".

Posted by Quantao on December 12, 2020

Peptide docking problem.

A web server to improve peptide docking reuslt.

Posted by Quantao on December 10, 2020

Break it to make it

A website to findout the "MAX" ring. Don't be baised when do your retrosynthesis

Posted by Quantao on December 07, 2020

NO PAINS with GAINS

Remove the PAINS as soon as possible to not wasting time and resources in new drug development.

Posted by Quantao on December 07, 2020

Win Respect with Stereochemistry!

Two tips help you be the smart guy in the room!

Posted by Quantao on December 05, 2020

Installing Chembl Web Client

The official cheml_webresource_clietn installation method introduced.

Posted by Quantao on December 04, 2020

Bash Inrodcution

Basic bash laguage and simple usage. Be careful not deleting files unintendedly.

Posted by Quantao on December 03, 2020

Tutorial on FEP by NAMD/2.13-mpi

A free energy pertubation validaiton was carried out in detail, using namd-2.13mpi.

Posted by Quantao on December 02, 2020

What is Free Energy Pertubation

General information about the free energy pertubaion and its logics in helping small molecule drug developmet.

Posted by Quantao on November 30, 2020

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