ml / ai / bio / drugs
-
IOCB Prague / Charles University
- Prague
- https://prankweb.cz
- @rdkbio
- in/radoslavkrivak
- https://scholar.google.cz/citations?user=mq86xg0AAAAJ
- @rdkbio.bsky.social
Organizations
@cusbgStarred repositories
A Python library for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions.
SELFormer: Molecular Representation Learning via SELFIES Language Models
Container image for P2Rank, machine learning based prediction of ligand binding sites from protein structure
[ICML 2026 GenBio Workshop] Official Implementation for "Harmonic Torsional Diffusion for Protein-Ligand Flexible Docking"
A benchmark of active-site-disrupted decoy enzymes for evaluating EC number prediction models
Counting-only algebraic and table fields for cryptic-pocket detection on the official CryptoBench receptor-only benchmark
Nextflow pipeline to do protein design tasks at the end of 2025.
A machine learning pipeline for predicting protein-ligand binding sites from PDB structures, inspired by the P2Rank approach. The pipeline extracts geometric, physicochemical and evolutionary featu...
Accelerating Open-Source Binding Affinity Predictions
Data curation for assay development
A VAE-based protein-ligand binding site template search tool
Jax Codebase for Evolutionary Strategies at the Hyperscale
Fork of open-source PyMOL molecular visualization system refactored to run in MacOS/iOS using Metal.
AI agent toolkit: unified LLM API, agent loop, TUI, coding agent CLI
Pi extension: a persistent second model that reviews the main agent's work each turn and injects concise advice inline.
SGX-ready Enclaive Docker Image for Nginx
High-performance SASA (Solvent Accessible Surface Area) calculation in Zig with Python bindings
Fast, lightweight reaction classification with high granularity
MolBench — a molecular-visualization benchmark & harness for CI (LLM) assistants: natural language → Mol*/ipymolstar API calls, graded deterministically, plus VLM-judged visual tasks.
Mol* chat-driver: natural-language prompts -> MolViewSpec scenes rendered in Mol*, with reliable prompt/feedback capture. Built for MolBench human evaluation. Free for non-commercial use.
Preliminary model report for the OpenADMET PXR Challenge
1
Updated Jul 2, 2026
Code used to mine surfaces.
A smarter cd command. Supports all major shells.