dlukauskis / OpenBPMDLinks
☆13Updated 3 months ago
Alternatives and similar repositories for OpenBPMD
Users that are interested in OpenBPMD are comparing it to the libraries listed below
Sorting:
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆24Updated 3 weeks ago
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Updated last year
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆25Updated last year
- ☆45Updated 3 weeks ago
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆18Updated last year
- ☆65Updated last year
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆45Updated 3 weeks ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆63Updated 4 months ago
- PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking☆34Updated 7 months ago
- Pocket dynamics analysis tool☆13Updated 3 weeks ago
- Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping☆34Updated last month
- This is the first model that can simultaneously predict the RMSD of the ligand docking pose and the binding strength against the target.☆18Updated 5 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- An open library to work with pharmacophores.☆45Updated last year
- Binding pocket optimization based on force fields and docking scoring functions☆33Updated 2 months ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 2 years ago
- ☆32Updated 2 years ago
- This Code is for Fragment-wise 3D Structure-based Molecular Generation with Reliable Geometry☆25Updated 2 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.☆49Updated 2 months ago
- ☆35Updated 2 months ago
- Official implementation of "PIGNet2: a versatile deep learning-based proteinligand interaction prediction model for binding affinity scor…☆18Updated 4 months ago
- Python package for the analysis of natural and modified peptides using a set of modules to study their sequences☆33Updated 4 months ago
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆16Updated 8 months ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 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.☆18Updated 3 weeks ago
- ☆12Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆12Updated 2 years ago