Contact map analysis for biomolecules; based on MDTraj
☆48Jan 25, 2026Updated 3 months ago
Alternatives and similar repositories for contact_map
Users that are interested in contact_map are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- These files are meant to accompany "What are our models really telling us? A practical tutorial on avoiding common mistakes when buildin…☆13May 22, 2013Updated 12 years ago
- An open source Python framework for transition interface and path sampling calculations.☆116Mar 23, 2026Updated last month
- Absolute solvation free energy calculations with OpenFF and OpenMM☆30Dec 1, 2024Updated last year
- A command line application to launch molecular dynamics simulations with OpenMM☆40Apr 7, 2022Updated 4 years ago
- A collections of scripts for working molecular dynamics simulations☆45Feb 6, 2026Updated 2 months 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.
- ☆15Jun 26, 2018Updated 7 years ago
- Differentiable Markov Chain Monte Carlo☆15Mar 23, 2024Updated 2 years ago
- Analysis of non-covalent interactions in MD trajectories☆68Jan 3, 2025Updated last year
- Collection of Python scripts to setup and run simulations with OpenMM☆17May 22, 2020Updated 5 years ago
- Software for automated processing of alchemical free energy calculations☆12Nov 7, 2022Updated 3 years ago
- Shape-based alignment of molecules using 3D point-based representation☆23Apr 8, 2026Updated 3 weeks ago
- Unified Free Energy Dynamics (UFED) simulations with OpenMM☆35Aug 20, 2025Updated 8 months ago
- A python toolkit for analysing membrane protein-lipid interactions.☆71Mar 30, 2026Updated last month
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆20Aug 14, 2020Updated 5 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.
- 📦 A Command Line Tool for downloading protein structures, sequences and MSAs☆10Nov 21, 2017Updated 8 years ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆25Jul 19, 2021Updated 4 years ago
- Introductory tutorial on TPS, committor analysis, and (MS)TIS with OpenPathSampling☆19Dec 15, 2025Updated 4 months ago
- Python script that creates 2D protein-ligand interaction images☆14Apr 23, 2018Updated 8 years ago
- 3D molecular structure generation for MD simulation☆10Apr 29, 2020Updated 6 years ago
- A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed b…☆10Nov 22, 2016Updated 9 years ago
- Scores for Hydrophobicity and Charges based on SASAs☆42Jun 12, 2025Updated 10 months ago
- Implementation of MOFF force field. Please cite us at Latham, A; Zhang, B J. Chem. Theory Comput. 2021, 17, 3134. (https://pubs.acs.org/d…☆10Jun 16, 2022Updated 3 years ago
- A Python toolkit for the analyis of lipid membrane simulations☆35Oct 24, 2025Updated 6 months 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.
- Multiscale Simulation Tool for Backmapping☆22Mar 13, 2026Updated last month
- An open set of tools for automating tasks relating to small molecules☆70Oct 27, 2021Updated 4 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆46May 3, 2021Updated 5 years ago
- APBS & PDB2PQR - software for biomolecular electrostatics and solvation☆31Jun 11, 2022Updated 3 years ago
- A library to perform targeted free energy perturbation with normalizing flows.☆11Sep 1, 2025Updated 8 months ago
- Containerised components for cheminformatics and computational chemistry☆36May 23, 2023Updated 2 years ago
- easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems an…☆36Mar 12, 2026Updated last month
- Normal Mode Analysis for Macromolecules☆18Apr 1, 2017Updated 9 years ago
- MDMS: Molecular Dynamics Made Simple; Python program facilitating performing Molecular Dynamics simulations of proteins☆27Oct 29, 2019Updated 6 years ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Jan 3, 2026Updated 4 months ago
- Real time monitoring and visualization of Amber MD simulations☆17Feb 6, 2020Updated 6 years ago
- MDAnalysis wrapper around Packmol☆37May 1, 2023Updated 3 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Feb 11, 2021Updated 5 years ago
- DISTEVAL: A web-server for evaluating protein inter-residue distances☆18Mar 7, 2022Updated 4 years ago
- A knowledge-based method for determining small molecule binding "hotspots".☆40May 3, 2024Updated 2 years ago
- High level API for using machine learning models in OpenMM simulations☆163Updated this week