freeenergylab / amber_tutorials
Some tutorials on how to use AMBER simulation package. Especially for Amber22+AmberTools23.
☆14Updated last week
Related projects ⓘ
Alternatives and complementary repositories for amber_tutorials
- A deep learning framework for predicting interactions between protein-protein interaction targets and modulators☆11Updated 11 months ago
- Incorporation of conformational space profile into molecular representation learning, and its application to drug discovery, including vi…☆38Updated this week
- ☆24Updated 7 months ago
- Binding pocket optimization based on force fields and docking scoring functions☆29Updated last week
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆17Updated 3 weeks ago
- ☆37Updated 10 months ago
- Graph variational encoders for drug engineering and potentiation☆26Updated last year
- Codes and scripts for "An artificial intelligence accelerated virtual screening platform for drug discovery"☆35Updated last month
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆27Updated 5 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆15Updated last week
- ☆16Updated 2 years ago
- ☆18Updated last year
- Cryptic pocket prediction using AlphaFold 2☆22Updated last year
- Use AutoDock for Ligand-based Virtual Screening☆19Updated 2 months ago
- InteractionGraphNet: a Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein-Ligand Interaction Predictio…☆43Updated last year
- scripts to find PBD structures for cancer driver proteins☆29Updated 8 months ago
- OnionNet-2 is constructed based on convolutional neural network (CNN) to predict the protein-ligand binding affinity.☆16Updated 8 months ago
- ☆18Updated last year
- Automatic gromacs protocol from preparation to production with ligand parametrization through☆59Updated last month
- MD pharmacophores and virtual screening☆32Updated 10 months ago
- ☆60Updated 10 months ago
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆21Updated 10 months ago
- DeepRMSD+Vina is a computational framework that integrates ligand binding pose optimization and screening.☆37Updated 9 months ago
- Integrative modeling of PROTAC-mediated ternary complex☆22Updated 2 years ago
- Screening protocol with AUTODOCK-GPU☆10Updated last year
- Scripts for virtual screening, cross docking and protein relax using Schrödinegr and Rosetta☆58Updated 3 weeks ago
- Python package for the analysis of natural and modified peptides using a set of modules to study their sequences☆22Updated 3 weeks 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
- dockECR: open consensus docking and ranking protocol for virtual screening of small molecules☆24Updated 3 years ago
- PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking☆29Updated last month