Python code to run Supervised Molecular Dynamics (SuMD) simulations
☆16Apr 24, 2024Updated last year
Alternatives and similar repositories for SuMD
Users that are interested in SuMD are comparing it to the libraries listed below
Sorting:
- Online solubility prediction tool (streamlit) that runs the top-performing ML model (AqSolPred).☆10Nov 11, 2024Updated last year
- ☆13Jul 11, 2023Updated 2 years ago
- Python module for identification of conserved water molecules from molecular dynamics trajectories.☆14Feb 12, 2026Updated 2 weeks ago
- A toolkit developed to predict and analyze PROTAC-mediated ternary complexes using AlphaFold3 and Boltz-1.☆40Jul 17, 2025Updated 7 months ago
- App for serotonergic targets☆12Jan 8, 2026Updated last month
- PepFun 2.0: improved protocols for the analysis of natural and modified peptides☆27Jul 7, 2023Updated 2 years ago
- Efficient Sampling of PROTAC-Induced Ternary Complexes☆12Jun 3, 2025Updated 8 months ago
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Jun 3, 2024Updated last year
- Fragment Linker Prediction Using Deep Encoder-Decoder Network for PROTAC Drug Design☆12Oct 2, 2023Updated 2 years ago
- Implementation for SuperWater☆39Jan 9, 2026Updated last month
- A Python program for QM/MM Simulations based on the Perturbed Matrix Method☆26Oct 17, 2023Updated 2 years ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆29Oct 22, 2025Updated 4 months ago
- Modelling protein conformational landscape with Alphafold☆55Aug 29, 2025Updated 6 months ago
- A PyMOL plugin with accompanying Docker image for kinase inhibitor binding and affinity prediction☆12Jun 3, 2024Updated last year
- ☆13Sep 4, 2021Updated 4 years ago
- Model to predict kinase-ligand pKi values.☆12Jul 6, 2023Updated 2 years ago
- A Deep Learning Framework for Allosteric Site Prediction☆15May 21, 2025Updated 9 months ago
- Supporting Information of Publications☆14Mar 24, 2019Updated 6 years ago
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆18Jun 30, 2025Updated 8 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- ☆14Jul 5, 2022Updated 3 years ago
- RNA Structural Bioinformatics Crash Course & Data Science in Python☆13Oct 19, 2022Updated 3 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Feb 19, 2026Updated last week
- DeepCoSI: a Structure-based Deep Graph Learning Network Method for Covalent Binding Site Identification.☆14Oct 22, 2023Updated 2 years ago
- ☆15Dec 4, 2023Updated 2 years ago
- Interface-aware molecular generative framework for protein-protein interaction modulators☆19Dec 22, 2024Updated last year
- ☆18Mar 13, 2024Updated last year
- Rapid Generation of Rare Event Pathways Using Direction Guided Adaptive Sampling: From Ligand Unbinding to Protein (Un)Folding☆38Nov 25, 2025Updated 3 months ago
- Data set of protein-ligand complexes with reliable experimental structures and affinities☆44Oct 2, 2025Updated 4 months ago
- Molecular Dynamics on Google Compute Engine, Colab, AWS (Amazon Web Services) and other Cloud Computing services☆23Oct 18, 2025Updated 4 months ago
- Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping☆47Jan 28, 2026Updated last month
- A deep learning framework for accurate reaction prediction and its application on high-throughput experimentation data☆17Aug 8, 2023Updated 2 years ago
- ☆17Sep 14, 2022Updated 3 years ago
- ☆18Jul 14, 2024Updated last year
- A comprehensive Model Context Protocol (MCP) server providing advanced access to the UniProt protein database.☆19Dec 21, 2025Updated 2 months ago
- Tutorial to build AMBER compatable protein+lipid systems☆16Apr 19, 2017Updated 8 years ago
- Multiscale Simulation Tool for Backmapping☆22Feb 7, 2026Updated 3 weeks ago
- De novo molecular design with deep molecular generative models for protein-protein interaction(PPI) inhibitors☆22Nov 6, 2024Updated last year
- A comprehensive Model Context Protocol (MCP) server for accessing the PubChem chemical database. This server provides access to over 110 …☆32Dec 21, 2025Updated 2 months ago