dooo12332 / AlphaTraj
Pocket dynamics analysis tool
☆12Updated last month
Alternatives and similar repositories for AlphaTraj:
Users that are interested in AlphaTraj are comparing it to the libraries listed below
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆36Updated 2 months ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆23Updated last month
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 2 years ago
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆23Updated last year
- ☆15Updated 8 months ago
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆27Updated 9 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- ☆18Updated 2 years ago
- ☆55Updated last year
- ☆11Updated last month
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆46Updated 4 months ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆22Updated 2 years ago
- ☆14Updated 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.☆16Updated 6 months ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- ☆12Updated last year
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Lightweight induced fit docking☆20Updated last year
- Fully automated high-throughput MD pipeline☆56Updated 3 weeks ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆16Updated 4 months ago
- ☆39Updated 7 months ago
- Different run and analysis scripts as described in the research guides.☆13Updated 2 years ago
- Binding pocket optimization based on force fields and docking scoring functions☆30Updated 3 months ago
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆22Updated 3 months ago
- An open library to work with pharmacophores.☆45Updated last year
- 3D ligand-based pharmacophore modeling☆49Updated last year