StructBioReasoner

Search and select enzyme sequence homologs from a database. Use when users provide a query sequence and want to discover sequence homologs of the query sequence in a database.

Scientific reasoning via Jnana CoScientist — hypothesis generation, evaluation, and parameter bounding

Molecular dynamics simulations using OpenMM with MDAgent-style automation and free energy calculations via MM-PBSA

Convert scientific papers into executable computational workflows and MCP tools

Protein language model embeddings, diversity sampling, and mutation prediction using ESM or GenSLM

Protein structure prediction using Chai-1 or AlphaFold with confidence scoring, quality assessment, and critic evaluation

Analysis of molecular dynamics trajectories (RMSD, RMSF, contacts, hotspot analysis)

Computational peptide binder design using BindCraft pipeline (ProteinMPNN inverse folding + Chai/ESMFold structure validation + energy scoring + quality control)

HPC-scale literature mining and retrieval-augmented generation for structural biology

Multiple sequence alignment and conservation analysis using MUSCLE