Stars
A curated list of awesome deep learning applications in the field of computational biology
Required LAMMPS and MATLAB files for several molecular dynamics simulations.
Julia Bindings for Atomic Simulation Environment
An unofficial Fabric port of the original ConnectedTexturesMod. Adds extensions to the vanilla model and texture system to allow resource packs to create complex models.
This repository contains the data and scripts necessary to reproduce the results presented in the paper: **"Scalable molecular simulation of electrolyte solutions with quantum chemical accuracy"** …
Tools for preparation and analysis of systems for molecular dynamics.
Recent development in Graphic Processing Units (GPUs) has opened a new challenge in harnessing their computing power as a new general-purpose computing paradigm with its CUDA parallel programming. …
This will let marathonMR package run on a large cluster through message passing interface (MPI). MPI is the most common way of using long running jobs on parallel such as Gromacs, NAMD, etc.
Exercise for the modeling of biological systems course.
.NET 4.0 Console App to browse VMDK / VHD images and extract files
Systems Modeling. Learn a variety of systems, such as those involving mechanical, electrical, hydraulic, pneumatic systems, and mixtures of these systems. Utilize Matlab/Simulink to model, simulate…
List of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning
Universal modeling and simulation of fluid mechanics upon machine learning. From the Boltzmann equation, heading towards multiscale and multiphysics flows.
Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD.
DEPRECATED - PyMol plugin for hydrogen bond and water 9106 wire analysis of crystal structures and MD simulations.
This repository contains the data preprocessing analysis scripts of the manuscript "Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues" by Eraslan …
Plug in and Play Implementation of Tree of Thoughts: Deliberate Problem Solving with Large Language Models that Elevates Model Reasoning by atleast 70%
Drop Dash (API): A home delivery platform that allows users to search for and purchase products from local restaurants near their homes, place orders, and schedule deliveries. Provides access to re…
A work-in-progress, open-source, multi-player city simulation game.
a deep learning architecture for protein-ligand binding affinity prediction
Some high performance computing in C and Fortran 90 using OpenMP and MPI. Includes starter examples, parallel Poisson solver, parallel particle mesh simulation, parallel 2d random walk, parallel Ba…
Fluid Java interface to OpenStreetMap data through querying the Overpass API
Molecular dynamics simulations of ionic polymer metal composites (IPMCs)
Source code associated with final project for Machine Learning Course (CS 229) at Stanford University; Used reinforcement learning approach in a SUMO traffic simulation environment