MDMS: Molecular Dynamics Made Simple; Python program facilitating performing Molecular Dynamics simulations of proteins
☆27Oct 29, 2019Updated 6 years ago
Alternatives and similar repositories for MDMS
Users that are interested in MDMS are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ProQDock is a Protein-Protein docking scoring program that uses high level coordinate driven features compiled and trained by a Support V…☆11Dec 11, 2021Updated 4 years ago
- MEGADOCK on Google Colaboratory☆20Oct 2, 2023Updated 3 years ago
- [WIP] Classical atomistic simulation engine with a focus on user-friendliness and extensibility☆11Aug 8, 2023Updated 3 years ago
- Bayesian Active Learning for Optimization and Uncertainty Quantification with Applications to Protein Docking☆13Apr 28, 2021Updated 5 years ago
- WaterDock-2.0 implementation with Akshay Sridhar☆22Nov 2, 2023Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A wxPython graphical interface for the PyRosetta and Rosetta protein modeling suites☆29May 23, 2018Updated 8 years ago
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆43Jun 19, 2026Updated 4 months ago
- ☆13Dec 29, 2022Updated 3 years ago
- mirror of https://zhanglab.ccmb.med.umich.edu/EDTSurf/☆10Jun 20, 2023Updated 3 years ago
- Genetic algorithm to convert 3D-RISM solvent densities to explicit water molecules in binding pockets☆13Dec 19, 2017Updated 8 years ago
- Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations in protein-protein and protein-ligand systems☆11Mar 30, 2022Updated 4 years ago
- ☆10Dec 4, 2021Updated 4 years ago
- Developing a Deep learning classification-based model for screening pharmaceutical compounds with hERG inhibitory activity (cardiotoxicit…☆15Oct 2, 2024Updated 2 years ago
- Learning protein representation for rigid-body docking☆22Nov 2, 2019Updated 6 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Gromacs molecular dynamics simulation analysis scripts☆10Apr 5, 2022Updated 4 years ago
- Dynamics PyMOL Plugin☆49Apr 19, 2024Updated 2 years ago
- Supporting Information for "Prediction of Organic Compound Aqueous Solubility Using Interpretable Machine Learning"☆13Jun 5, 2023Updated 3 years ago
- GenUI frontend application. It provides a GUI to the GenUI REST API web services.☆23Sep 4, 2023Updated 3 years ago
- Binding pocket optimization based on force fields and docking scoring functions☆40Mar 19, 2025Updated last year
- ☆10May 17, 2021Updated 5 years ago
- Real time monitoring and visualization of Amber MD simulations☆16Feb 6, 2020Updated 6 years ago
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13May 12, 2026Updated 5 months ago
- An Interface-Predicting Language Model for Designing Peptide-Guided Protein Degraders☆18Sep 10, 2024Updated 2 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Python package to manage protein structures and their annotations☆46Mar 18, 2026Updated 7 months ago
- An integrated web-based platform for molecular descriptor and fingerprint computation☆13Nov 9, 2016Updated 9 years ago
- Input- hand-drawn image of molecule... Output- SMILES format molecule name☆16Apr 23, 2019Updated 7 years ago
- ☆57Aug 3, 2024Updated 2 years ago
- A Deep-learning based dOcking decoy eValuation mEthod☆58May 12, 2023Updated 3 years ago
- Kinase-focused fragment library☆69Jun 3, 2026Updated 4 months ago
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- Protein surface topographical mapping tool☆29Aug 17, 2023Updated 3 years ago
- DSResSol: A sequence-based solubility predictor created with Dilated Squeeze Excitation Residual Networks☆12May 30, 2024Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Generation of new putative Mdmx inhibitors from scratch based on Recurrent Neural Networks and molecular docking.☆10Jun 27, 2019Updated 7 years ago
- Mirror of https://codeberg.org/rvhonorato/gdock >> development happens on Codeberg☆20Jul 7, 2026Updated 3 months ago
- Pytorch implementation of Pocket2Drug: a generative deep learning model to predict binding drugs for ligand-binding sites.☆22May 19, 2022Updated 4 years ago
- Contact map analysis for biomolecules; based on MDTraj☆50May 9, 2026Updated 5 months ago
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆21Oct 11, 2021Updated 5 years ago
- ☆30Apr 2, 2026Updated 6 months ago
- Code and analyses related to the ExaLearn drug design efforts☆11Sep 30, 2020Updated 6 years ago