sahakyanhk / iPBSALinks
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
Sorting:
- ☆14Updated 3 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Updated last year
- OnionNet-2 is constructed based on convolutional neural network (CNN) to predict the protein-ligand binding affinity.☆19Updated last year
- A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening☆29Updated 2 months ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Updated 5 months ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years ago
- ☆25Updated last year
- ☆50Updated 3 months ago
- Code used to mine surfaces.☆20Updated 5 months ago
- Machine Learning Boosted Docking (HASTEN): Accelerate Structure-based Virtual Screening☆39Updated last year
- Open source code for DyScore☆20Updated 2 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- ☆28Updated 3 months ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 3 months ago
- Screening protocol with AUTODOCK-GPU☆13Updated 2 years ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated 4 months ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆70Updated 7 months ago
- DSDPFlex: Flexible-Receptor Docking with GPU Acceleration☆23Updated last month
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆19Updated 2 months ago
- 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
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆57Updated 3 months ago
- Optimization of binding affinities in chemical space for drug discovery☆35Updated 2 years ago
- ☆16Updated last year
- ☆16Updated 9 months ago
- PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking☆34Updated 10 months ago
- ☆22Updated 5 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 4 months ago