dooo12332 / AlphaTrajLinks
Pocket dynamics analysis tool
☆13Updated last month
Alternatives and similar repositories for AlphaTraj
Users that are interested in AlphaTraj are comparing it to the libraries listed below
Sorting:
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆24Updated last month
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆66Updated 5 months ago
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆25Updated last year
- This script is designed for evaluating the binding affinity between a protein target and a small molecule, by calculating the binding fre…☆13Updated 2 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 2 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- Different run and analysis scripts as described in the research guides.☆13Updated 2 years ago
- ☆14Updated 3 years ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- ☆11Updated last year
- ☆13Updated 4 months ago
- DirectMultiStep: Direct Route Generation for Multistep Retrosynthesis☆19Updated last month
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Updated last year
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆55Updated 2 months ago
- ☆12Updated last year
- ☆65Updated last year
- Cryptic pocket prediction using AlphaFold 2☆23Updated 2 years ago
- Binding pocket optimization based on force fields and docking scoring functions☆33Updated 3 months ago
- Code used to mine surfaces.☆15Updated 4 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.☆50Updated 2 months ago
- ☆16Updated 11 months ago
- ☆47Updated last month
- 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
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆12Updated 2 years ago
- 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
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆46Updated last month
- A tutorials suite for BioSimSpace.☆25Updated last month
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆23Updated 6 months ago
- ☆10Updated 5 years ago