AI Models and Modeling Tools for BioJazz Lab

Maintained by: BioJazz Lab, Department of Biology, Baylor University
Last updated: 2026-10-27
Purpose: Track AI/ML models relevant to BioJazz Lab research — phage-host interactions, genome-scale metabolic modeling, PTM-driven biomolecular assembly, and multi-scale eco-evolutionary dynamics.

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Table of Contents

1. Protein Modeling & Design
2. Molecular Dynamics & Conformational Sampling
3. Molecular Docking & Binding Affinity
4. Genomics & Metagenomics
5. Metabolic Modeling & Systems Biology
6. Phage Biology & Viromics
7. Multi-omics & Proteomics
8. Virtual Cell & Cell Simulation
9. Computational Tools & Algorithms

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Protein Modeling & Design

Model	Description	Access	Notes
AlphaFold3	Structure prediction for proteins, DNA, RNA, ligands, ions	AlphaFold Server / GitHub	Best for single-chain and complex structures; supports PTMs
OpenFold3	Open-source community reimplementation of AlphaFold3 (permissive license)	GitHub	Enables training and fine-tuning; basis for AQAffinity
RomeroLab/lightning-boltz	PyTorch Lightning training framework for Boltz-1/2; biomolecular structure prediction	GitHub	MIT-licensed; strong AlphaFold3 alternative for proteins, DNA, RNA, small molecules
ESMC (ESM Cambrian)	Protein language model (300M & 600M params); sequence representation, function prediction, embeddings	GitHub / HuggingFace	Successor to ESM-2; Dec 2024; no MSA needed; strong zero-shot function annotation
ESMFold2	Fast single-sequence protein structure prediction; successor to ESMFold	GitHub / Biohub	EvolutionaryScale / CZ Biohub; no MSA; suitable for large-scale metagenomic screening
ESM-3	Multimodal protein model (sequence, structure, function)	GitHub	Supports conditional generation; useful for design
ProtTrans (ProtBERT, ProtT5)	Protein sequence embeddings via transformer	GitHub / HuggingFace	Good for representation learning; classification tasks
RoseTTAFold2 / RoseTTAFold-All-Atom	Structure prediction; supports small molecules	GitHub	Handles non-protein atoms well
ProteinMPNN	Inverse folding / sequence design from backbone	GitHub	Useful for engineering phage tail fibers or enzymes
SaProt	Structure-aware protein language model	GitHub	Combines sequence + structure tokens
RFD4-Proteina	Generative diffusion model for de novo protein design (NVIDIA + UW Institute for Protein Design; successor to RFDiffusion)	GitHub / HuggingFace / NVIDIA NIM	2026; open-weight; state-of-the-art backbone design
se3_diffusion (FrameDiff)	SE(3) diffusion model for de novo protein backbone generation	GitHub	Generates diverse backbone scaffolds; ICML 2023
RigidSSL	Rigidity-aware geometric pretraining for protein design and conformational ensembles	GitHub / ICLR 2026	SSL using rigid body augmentation; improves design and ensemble prediction
FoldDisco	Ultra-fast discontinuous structural motif search across the protein universe	GitHub	From Steinegger lab; indexes and queries billions of structures
PhosphoSitePlus ML tools	PTM site prediction	PhosphoSitePlus	Relevant for PTM-driven assembly project
DeepPhos / NetPhos	Phosphorylation site prediction	NetPhos	Classical PTM prediction

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Molecular Dynamics & Conformational Sampling

Model	Description	Access	Notes
ConforNets	Latent-based conformational control built on OpenFold3; generates and steers protein conformational ensembles	GitHub / arXiv	From aqlaboratory (OpenFold3 team); 2026
BioEmu2	Microsoft generative model for protein equilibrium conformational ensemble emulation	GitHub / HuggingFace	Replaces costly MD simulations for ensemble generation; thermodynamically grounded
yesint/molar	Rust + Python library for high-performance reading and analysis of MD trajectories	GitHub / Docs	Supports GROMACS, AMBER formats; fast alternative to MDAnalysis for large trajectories
David-OConnor/dynamics	Rust-based molecular dynamics simulation engine	GitHub / Docs	Lightweight MD library; useful for custom simulation workflows

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Molecular Docking & Binding Affinity

Model	Description	Access	Notes
DiffDock	Diffusion-based protein–ligand docking	GitHub	State-of-the-art blind docking; relevant for enzyme–metabolite interactions
DiffDock-Glide	DiffDock pose sampling combined with Schrödinger Glide scoring for improved accuracy	GitHub	Hybrid approach; Glide rescoring improves pose selection
SurfDock	Surface-informed diffusion model for protein–ligand complex prediction; uses molecular surface geometry to guide pose sampling	GitHub / Nature Methods	Published Nature Methods 2024; strong blind docking benchmark performance
AQAffinity	Structure-free binding affinity prediction built on OpenFold3 (SandboxAQ)	SandboxAQ / Docs	High-speed drug potency prediction without requiring a solved structure; 2026

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Genomics & Metagenomics

Model	Description	Access	Notes
Nucleotide Transformer (NT)	DNA language models (500M–2.5B) for genomic sequences	GitHub / HuggingFace	Broad genomic tasks: variant effect, regulatory elements
DNABERT-2	Multi-species DNA foundation model	GitHub	Better than DNABERT-1; tokenization improvements
Evo2	DNA language model (7B & 40B params) trained on 9.3 trillion nucleotides across all domains of life; prokaryote, phage, and eukaryote genomes	GitHub	Arc Institute + NVIDIA; particularly relevant for phage-host research
HyenaDNA	Long-range DNA model (up to 1M context)	GitHub	Long genomic context; efficient architecture
Caduceus	Bidirectional, long-range DNA model	GitHub	State-space model; strong on genomic benchmarks
MMseqs2	Ultra-fast many-against-many protein/nucleotide sequence search and clustering	GitHub	Essential for large-scale homology search and metagenomic annotation; orders of magnitude faster than BLAST
MMseqs2-GPU	GPU-accelerated MMseqs2 for massive-scale sequence search and clustering	GitHub	Same interface as MMseqs2; dramatically faster on GPU nodes; ideal for HPC metagenomics workflows
GenoME	Metagenomic classification and embedding	—	Useful for microbiome studies
DeepMicro	Deep learning for microbiome phenotype prediction	GitHub	Relevant for eco-evolutionary microbiome work

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Metabolic Modeling & Systems Biology

Model	Description	Access	Notes
MICOM	Community metabolic modeling (flux balance)	GitHub	Multi-species FBA; relevant for microbial community metabolism
DLKcat	Deep learning–based kcat (enzyme turnover) prediction	GitHub	Useful for parameterizing GEMs
UniKP	Unified enzyme kinetics prediction (kcat, Km, Ki)	GitHub	Broader than DLKcat
TurNuP / NNKD	kcat/Km prediction from sequence + substrate	—	Alternative kinetics tools
FluxML / COBRA.py	Constraint-based metabolic modeling frameworks	GitHub	Core tools for genome-scale metabolic models
gpuGEM	GPU-accelerated linear optimization for genome-scale metabolic models via NVIDIA cuOpt	arXiv	1.1–94× faster than HiGHS; MIT-licensed; pip install gpugem; requires Volta+ GPU, CUDA 12, cuOpt 26.6+
GEM-PRO	Structure-aware GEM construction	GitHub	Links protein structure to metabolic models
AutoML-GEM	ML-guided GEM refinement	—	Gap-filling and curation
DeepEC	EC number prediction from sequence	GitHub	Useful for annotating metabolic genes
ECRECer	Enzyme commission number prediction	GitHub	Alternative to DeepEC

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Phage Biology & Viromics

Model	Description	Access	Notes
PhaTYP	Phage lifestyle (lytic/lysogenic) prediction	GitHub	Relevant for phage-host interaction studies
CHERRY	Phage-host interaction prediction	GitHub	Direct phage-host linkage from sequence
iPHoP	Integrated phage-host prediction	GitHub	Ensemble approach; recommended for metagenomics
DeepHost	Deep learning phage host range prediction	GitHub	Sequence-based host prediction
VirSorter2	Virus identification in metagenomic data	GitHub	Standard virome discovery tool
VIBRANT	Virus identification and annotation	GitHub	Good for viral metabolic annotation
CheckV	Quality assessment of viral genomes	GitHub	Essential QC before downstream analysis
PhageAI	Phage lifecycle AI platform	PhageAI	Commercial; useful for classification
Evo2 (phage-tuned)	Generative model for phage and viral sequence design; zero-shot functional sequence generation	GitHub	Arc Institute + NVIDIA; strong zero-shot generalization to phage proteins

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Multi-omics & Proteomics

Model	Description	Access	Notes
Prosit	Peptide fragmentation and retention time prediction	GitHub / Prosit Server	Enhances MS/MS database search
AlphaPeptStats	Statistical analysis of proteomics data	GitHub	From Mann lab; PTM-aware
MSBooster	Deep learning–rescoring for proteomics	GitHub	Integrates with FragPipe pipeline
DeepMass:Prism	Deep learning for proteomics data analysis	—	Spectral library generation
MOFA+	Multi-omics factor analysis	GitHub	Integrates transcriptomics, proteomics, metabolomics
scVI / scANVI	Single-cell multi-omics integration	GitHub	Latent variable models for sc data
totalVI	Protein + RNA joint modeling (CITE-seq)	scvi-tools	Part of scvi-tools ecosystem
UnitedNet	Multi-modal single-cell data integration	GitHub	Transfer between modalities

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Virtual Cell & Cell Simulation

Model	Description	Access	Notes
scGPT	Single-cell foundation model (33M cells pre-trained); cell type annotation, perturbation prediction, GRN inference	GitHub	Strong zero-shot generalization across tissues
Geneformer	Transformer pre-trained on 30M single-cell profiles; in silico gene perturbations	HuggingFace	Predicts knockout effects without experiments
scFoundation	Large-scale single-cell foundation model (100M+ cells)	GitHub	Strong cross-tissue and cross-condition generalization
UCE (Universal Cell Embeddings)	Zero-shot single-cell embeddings; works across species without fine-tuning	GitHub	Useful for cross-organism eco-evolutionary comparisons
GEARS	Graph-based model for predicting single and combinatorial genetic perturbations	GitHub	Predicts unseen perturbation outcomes from sc data
CellOracle	GRN inference + TF perturbation simulation from scRNA/scATAC	GitHub	Simulates cell fate changes; links GRN to cell identity
SCENIC / SCENIC+	Gene regulatory network inference from scRNA-seq and scATAC-seq	GitHub	SCENIC+ integrates chromatin accessibility for GRN
NicheNet	Cell–cell communication via ligand–target inference	GitHub	Predicts intercellular signaling; relevant for phage-host and host–microbe contexts
CellChat	Quantitative inference of cell–cell signaling networks at pathway level	GitHub	Complements NicheNet; good for microbial community signaling
scBERT	BERT-based model for single-cell cell type annotation	GitHub	Pre-trained on PanglaoDB
CellTypist	Automated cell type classification with curated model zoo	GitHub	Fast inference; many pre-built tissue models
AIDO.Cell	AI-driven cell foundation model for multi-modal sequence-to-cell prediction	GitHub	Emerging; multi-task model spanning sequence to phenotype
Cell2Sentence	Translates single-cell expression data to/from natural language via LLMs	GitHub	Bridges LLM reasoning with single-cell biology
Cellpose	Deep learning segmentation of cells in 2D/3D images	GitHub	Core tool for imaging-based phenomics and spatial omics
PhysiCell	Agent-based multicellular simulation (mechanistic, not ML)	GitHub	Integrates with ML outputs for whole-tissue spatial modeling
LatticeMicrobe	GPU-accelerated stochastic whole-cell simulation via RDME; spatial reaction-diffusion in realistic cell geometries	luthey-schulten.chemistry.illinois.edu	From Luthey-Schulten lab (UIUC); designed for bacterial/microbial cell modeling
Smoldyn	Spatial stochastic simulator for cell biology; models molecular diffusion, reactions, and membrane interactions in 3D	GitHub / smoldyn.org	Rule-based spatial simulation; integrates with SBML/BioNetGen
Virtual Cell (VCell)	ODE/PDE/stochastic simulation of intracellular dynamics with spatial support	vcell.org	NRBSC platform; useful for mechanistic signaling models
BioNetGen / PyBNG	Rule-based modeling of biochemical reaction networks	GitHub	Signaling network simulation; pairs well with parameter estimation tools (cf. pyModEst)

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Computational Tools & Algorithms

Tool	Description	Access	Notes
bigraph-rs	Rust implementation of bigraph data structures (bigraphical reactive systems)	GitHub / Docs	Formal graph model for concurrent biological systems; useful for network topology analysis

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Contributing & Conventions

• Add a new row to the relevant table; include model name (bold), a brief description, an access link, and notes specific to BioJazz Lab use cases.
• Mark deprecated or superseded models with strikethrough.
• For models actively in use in the lab, add a ✅ to the Notes column.
• Update the Last updated date at the top when making changes.

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For questions or suggestions, contact Song Feng (song.zhimu.feng@gmail.com).