sahakyanhk / iPBSA
iPBSA minimizes docked receptor-ligand conformations in implicit solvent and calculates the binding free energy with MM/PB(GB)SA methods. The algorithm is based on a freely available AmberTools18 which can be easily installed via conda
☆13Updated last year
Alternatives and similar repositories for iPBSA:
Users that are interested in iPBSA are comparing it to the libraries listed below
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆23Updated 4 months ago
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Updated 10 months ago
- ☆25Updated last year
- ☆10Updated 5 years ago
- A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening☆24Updated last week
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆11Updated 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…☆15Updated 10 months ago
- ☆28Updated 10 months ago
- ☆21Updated 4 months ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 2 years ago
- ☆21Updated 2 months ago
- ☆14Updated 2 years ago
- PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking☆34Updated 6 months ago
- Pocket dynamics analysis tool☆12Updated last week
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated 2 weeks ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆23Updated last week
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆18Updated 3 weeks ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 5 months ago
- OnionNet-2 is constructed based on convolutional neural network (CNN) to predict the protein-ligand binding affinity.☆17Updated last year
- Binding pocket optimization based on force fields and docking scoring functions☆31Updated last month
- ☆26Updated 5 months ago
- SIEVE-Score: interaction energy-based virtual screening method based on random forest.☆15Updated last year
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆61Updated 3 months ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆23Updated 2 years ago
- AI-augmented R-group exploration in medicinal chemistry☆16Updated 7 months ago
- InteractionDrawer is a JavaScript library for the drawing of highly interactive 2D ligand interaction diagrams.☆20Updated last year
- ☆12Updated last year
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆24Updated last year