molecularmodelingsection / TTMDLinks
Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations
☆19Updated 10 months ago
Alternatives and similar repositories for TTMD
Users that are interested in TTMD are comparing it to the libraries listed below
Sorting:
- ☆48Updated 2 months ago
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆48Updated 2 months ago
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆23Updated 2 weeks ago
- Fully automated high-throughput MD pipeline☆61Updated 3 weeks ago
- Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping☆35Updated last month
- Binding pocket optimization based on force fields and docking scoring functions☆33Updated 3 months ago
- moldrug (AKA mouse) is a Python package for drug-oriented optimization on the chemical space ☆37Updated 3 weeks ago
- Cryptic pocket prediction using AlphaFold 2☆23Updated 2 years ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 2 months ago
- Lightweight induced fit docking☆21Updated 2 years ago
- Quick mapping of Uniprot sequences to PDB structures☆32Updated 3 months ago
- ☆12Updated 2 years ago
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Updated last year
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆49Updated this week
- ☆68Updated last year
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆67Updated 6 months ago
- ☆21Updated 5 months ago
- Input files for GROMACS tutorials written for the Journal of Physical Chemistry B☆20Updated 11 months ago
- Weighted Ensemble Data Analysis and Plotting☆24Updated 3 weeks ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆29Updated 4 months ago
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆19Updated last year
- scripts to find PBD structures for cancer driver proteins☆31Updated 4 months ago
- All in one Structure-Based Virtual Screening workflow based on the concept of consensus docking.☆47Updated 5 months ago
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆18Updated 9 months ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆71Updated 5 months ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆18Updated 2 months ago
- A python module to plot secondary structure schemes☆25Updated last year
- Implementation of the Paper "iScore: A ML-Based Scoring Function for de novo Drug Discovery" by S.J. Mahdizadeh, and L.A. Eriksson (https…☆16Updated last year
- PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking☆34Updated 9 months ago