dooo12332 / AlphaTraj
Pocket dynamics analysis tool
☆12Updated last month
Related projects: ⓘ
- ☆38Updated 2 months ago
- ☆53Updated last year
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆10Updated 2 years ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆11Updated last month
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆46Updated last month
- 3D ligand-based pharmacophore modeling☆45Updated last year
- Computational Chemistry Workflows☆52Updated 2 years ago
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆27Updated 3 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated 9 months ago
- ☆14Updated 2 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆26Updated 2 months ago
- ☆25Updated 8 months ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆41Updated last month
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆51Updated last year
- ☆10Updated last year
- ☆14Updated 2 years ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated last year
- Scripts for running alchemical, free-energy perturbation simulations using Gromacs☆13Updated 6 years ago
- Lightweight induced fit docking☆19Updated last year
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆18Updated 8 months ago
- ☆28Updated 3 months ago
- ☆45Updated 9 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆15Updated 2 weeks ago
- Thompson Sampling☆49Updated 2 months ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆22Updated last year
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆73Updated last year
- Binding pocket optimization based on force fields and docking scoring functions☆28Updated 3 months ago
- binding free energy estimator 2☆101Updated last month
- Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina☆36Updated this week
- An open library to work with pharmacophores.☆34Updated last year