keisuke-yanagisawa / exprorerLinks
EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation
☆11Updated 2 years ago
Alternatives and similar repositories for exprorer
Users that are interested in exprorer are comparing it to the libraries listed below
Sorting:
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆50Updated 3 months ago
- ☆25Updated last year
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 2 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- Pocket dynamics analysis tool☆15Updated 2 months ago
- Code used to mine surfaces.☆19Updated 4 months ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆67Updated 6 months 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 2 weeks ago
- Computation of the drug-target relative residence times from RAMD simulations☆16Updated 10 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 2 weeks ago
- An open library to work with pharmacophores.☆45Updated 2 years ago
- ☆16Updated last year
- 3D ligand-based pharmacophore modeling☆49Updated 2 months ago
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆18Updated 9 months ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- ☆65Updated last year
- AI-augmented R-group exploration in medicinal chemistry☆17Updated 9 months ago
- Code to perform scaffold hopping and virtual screening using WHALES descriptors.☆31Updated 4 years ago
- DirectMultiStep: Direct Route Generation for Multistep Retrosynthesis☆20Updated 2 months ago
- ☆17Updated 2 years ago
- ☆14Updated 3 years 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 2 months ago
- A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening☆29Updated last month
- ☆17Updated last year
- ☆39Updated 11 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- ☆12Updated 2 years ago