sbm-tools is a simple python package for creating, modifying, and maintaining input files for native Structure-Based Model simulations to be used with the popular simulation software GROMACS.
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Updated
Mar 11, 2020 - Python
sbm-tools is a simple python package for creating, modifying, and maintaining input files for native Structure-Based Model simulations to be used with the popular simulation software GROMACS.
Source code and data for fast folding reduction algorithm
Python library for implementing geometrical representations of curves.
Protein folding is the physical process by which a protein chain attains its functional three-dimensional structure from a simple sequence of amino acids.
Code used for our paper, Variable Regions of p53 Isoforms Allosterically Hard Code DNA Interaction
A proof-of-concept for using AlphaFold with new amino acid sequences (this may change to a full project in the future).
Exploring Uniform Random Sampling in HP Model Protein Folding
Classifying protein binding sites from the Cyclica dataset. Built for the CxC 2023 Datathon
Your open-source alternative to AlphaFold3🚀
Lightning-Fast Template-free Protein Folding based on Predicted Residue Contacts and Secondary Structure
Hybridized distance- and contact-based hierarchical protein folding
CA-2-HCOMB is a tool for simplifying single-chain protein structures from PDB files into manageable models like various honeycombs, retaining essential information for in-depth computations. It's efficient for large datasets and machine learning, and user-friendly for research and education.
Python code for simulating protein folding using Monte Carlo and analyzing the structure with MDTraj and Bio.PDB
Examples for SDAccel 2017.1+ on AWS F1 instances
"Train Your Reinforcement Learning Algorithm To This Protein Folding Problem Simulation". This is part of my bachelor thesis. The latest version of this env is in the LogDQN_ProteinHP repository.
The working repository for my bachelor thesis with title : "LOGDQN DEEP REINFORCEMENT LEARNING IMPLEMENTATION FOR SOLVING HYDROPHOBIC-POLAR MODEL PROTEIN FOLDING PROBLEM (Tendean et al, 2020)"
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