John-Jumper / Upside-MDLinks
Coarse-grained molecular dynamics for protein physics
☆41Updated 8 years ago
Alternatives and similar repositories for Upside-MD
Users that are interested in Upside-MD are comparing it to the libraries listed below
Sorting:
- Fast, accurate, and deterministic protein side-chain packing☆37Updated 8 months ago
 - An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM☆37Updated 5 months ago
 - ☆74Updated 2 weeks ago
 - ☆45Updated this week
 - Modeling with limited data☆59Updated 3 months ago
 - Calculation of interatomic interactions in molecular structures☆109Updated last year
 - Adding hydrogens to molecular models☆50Updated last month
 - FreeSASA Python Module☆57Updated 2 months ago
 - A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dicti…☆69Updated 2 weeks ago
 - Modeling molecular ensembles with scalable data structures and parallel computing☆36Updated this week
 - A simple Python library to generate model peptides☆88Updated 4 years ago
 - ☆69Updated last year
 - Associative memory, Water mediated, Structure and Energy Model (AWSEM) protein simulation code☆41Updated 5 months ago
 - A lightweight pure python package for reading, writing and manipulating mmCIF files distributed by the wwPDB"☆38Updated 2 years ago
 - ☆32Updated last year
 - An application for configuring and running simulations with OpenMM☆74Updated this week
 - Trusted force field files for gromacs☆61Updated last year
 - Tutorials for non-Markovian dynamic models (qMSM and IGME) to study protein dynamics.☆26Updated last year
 - Tutorials and data necessary to reproduce the results of publication Machine Learning Coarse-Grained Potentials of Protein Thermodynamics☆90Updated 9 months ago
 - TMol☆47Updated this week
 - Best practice document for alchemical free energy calculations going to livecoms journal☆79Updated 3 weeks ago
 - Contact map analysis for biomolecules; based on MDTraj☆46Updated 10 months ago
 - PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.☆144Updated 8 months ago
 - A primer on statistical mechanics for biochemists☆47Updated 3 years ago
 - OpenMM implementation of MOFF, MRG-CG, and HPS models.☆32Updated 5 months ago
 - Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆66Updated 4 years ago
 - Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation☆132Updated 2 years ago
 - Structure prediction and design of proteins with noncanonical amino acids☆108Updated 2 weeks ago
 - Integrating Molecular Simulation and Experimental Data☆25Updated 4 years ago
 - Software for biomolecular electrostatics and solvation calculations☆115Updated last year