Sang's Projects
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
OpenMM is a toolkit for molecular simulation using high performance GPU code.
Designed to optimize the time/accuracy trade-off in predicting the effects of mutations on protein-protein binding
packmem: a tool to compute interfacial packing defects in simulated membranes
Work that is in development, but ones I want to show.
Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
C++ Programming Tutorial in Chemistry
Modern and fast molecular analysis and modeling library for C++ and Python
Python tool for performing coarse-grain mapping and model generation from atomistic molecular dynamics trajectories.
Analysis of non-covalent interactions in MD trajectories
🚂 Python API for Emma's Markov Model Algorithms 🚂
A Python Toolkit for Scalable Outlier Detection (Anomaly Detection)
A starter kit for publishing a python package
Folder containing the analysis code in C++/Python in MARTINI or SDK
PhD Molecular Dynamics Analysis Code - updated daily
This is a C version of the SCF code found in Appendix B of Modern Quantum Chemistry, An Introduction to Electronic Structure Theory by A. Szabo and N. Ostlund. I have included a built executable "scf_basic_version_1_0" and an output file called "out" which lists the results. Run the command "make" to build this. Note that this software is not designed to be either efficient in terms of performance or in terms of coding. It is designed as a bit of fun to convert the original Fortran IV code into something a bit more modern - C and also to demonstrate the key principles of the SCF routine when calculating the HeH+ molecule. Limited to STO-nG (n=1, 2 or 3) series basis set and 2 atoms only.
How to make seaborn plots in R
This is a short tutorial showing how to use both VMD and MDAnalysis to analyse a molecular dynamics simulation of a membrane protein.
A primer on software development best practices for computational chemistry
Supplementary information regarding NP topologies in GROMACS
C Practise as I am a bit rusty..
Time-Series Cross-Validation Module
Software, script and documentation repository for the UCL Collagen Group.
VOTCA's next generation build system
Testing django templates