New tools

SurfDock

SurfDock is a surface-informed diffusion generative model for protein-ligand docking, published in Nature Methods 2024. It leverages protein surface geometry to guide a diffusion process for reliable and accurate protein-ligand complex prediction.

protein-dockingstructure-prediction+5

SigmaDock

SigmaDock is a fragment-based molecular docking tool using SE(3) equivariant diffusion models to predict how small molecule ligands bind to protein targets. Presented at ICLR 2026, it generates multiple binding poses with Vinardo scoring.

protein-dockingdiffusion-model+5

Ligand fixer

Fix ligand files that fail RDKit, Meeko, or docking preparation. Repair SDF, MOL, and MOL2 inputs, apply safe chemistry cleanup, and export docking-ready SDF files.

structure-analysisquality-validation+3

Salmon

Quantify transcript abundance from RNA-seq reads with Salmon selective alignment. Upload a transcript FASTA reference plus single-end or paired-end FASTA/FASTQ reads to produce TPM and estimated read-count tables.

sequence-analysisstatistical+4

SuperWater

Predict protein hydration sites from a structure using a diffusion model with ESM features and a confidence-filtering head.

structure-analysisai-powered+4

IntelliFold 2

Controllable biomolecular structure prediction model for proteins, ligands, DNA, RNA, and multi-component complexes. IntelliFold 2 supports fast v2-Flash inference, optional MSA generation, and ranked confidence outputs.

protein-foldingai-powered+5