Zachary Martinez

propka. PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

posebusters. Plausibility checks for generated molecule poses.

PLACER. PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.

BindFlow. A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS

MAGPIE. MAGPIE

IPSAE. Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3

zoplicate. A plugin that does one thing only: Detect and manage duplicate items in Zotero.

FoldBeast. 3Di substitution models for BEAST 2

melonnpan. Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

biobakery. bioBakery tools for meta'omic profiling

metawibele. MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

fugassem. FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in Microbiomes

gapseq. Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

DRAM. Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

humann. HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

zDB. zDB: comparative bacterial genomics made easy

pnabind. A python package and collection of scripts for computing protein surface meshes, chemical, electrostatic, geometric features, and building/training graph neural network models of protein-nucleic acid binding

boltzgen. BoltzGen: Toward Universal Binder Design

CLAPE. contrastive learning and pre-trained encoder for protein-ligand binding sites prediction

cath-tools-genomescan. CATH: high-throughput protein structure/function annotations

PLM-interact. PLM-interact: extending protein language models to predict protein-protein interactions.

folddisco. Fast indexing and search of discontinuous motifs in protein structures

BattyBirdNET-Pi. A realtime acoustic bat & bird classification system for the Raspberry Pi 4/5 built on BattyBirdNET-Analyzer.

BattyBirdNET-Analyzer. BattyBirdNET analyzer for scientific audio data processing.

pi-hole. A black hole for Internet advertisements

BirdNET-Pi. A realtime acoustic bird classification system for the Raspberry Pi 5, 4B 3B+ 0W2 and more. Built on the TFLite version of BirdNET.

All-Atom-Protein-Sequence-Generation. Python

PocketVina. GPU-accelerated protein-ligand docking with automated pocket detection, exploring through multi-pocket conditioning. Official Implementation of PocketVina

plaid. All-atom protein generation using latent diffusion, with compositional function and taxonomic prompts. http://bit.ly/plaid-proteins

hierarchical_diffusion_LM. Python

MADSci. Main repository for the Modular Autonomous Discovery for Science (MADSci) Framework

faker. Faker is a Python package that generates fake data for you.

BAT.py. The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RBFE) calculations on protein-ligand systems, compatible with the AMBER and OpenMM simulation packages.

direct-file. Direct File

evo2. Genome modeling and design across all domains of life

BoltzDesign1. Python

masif_seed. Masif seed paper repository

CataPro. A generalized enzyme kinetics parameter prediction model.

SpeedPPI. Rapid protein-protein interaction network creation from multiple sequence alignments with Deep Learning

ProLIF. Interaction Fingerprints for protein-ligand complexes and more

bioemu. Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning

merizo_search. Fast protein domain structure embedding+search tool

genomad. geNomad: Identification of mobile genetic elements

reseek. Protein structure alignment and search algorithm

BindCraft. User friendly and accurate binder design pipeline

CatPred. Machine Learning models for in vitro enzyme kinetic parameter prediction

GraphEC. Python

ParmEd. Parameter/topology editor and molecular simulator

Insane. INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems

GraphSol. Code of our JC paper: "Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map"

caltechdata_api. Python library for using the CaltechDATA API

Racer. C

prevent-nf. PREVENT: PRotein Engineering by Variational frEe eNergy approximaTion

chai-lab. Chai-1, SOTA model for biomolecular structure prediction

PSICHIC. PSICHIC (pronounced Psychic) - PhySIcoCHemICal graph neural network for learning protein-ligand interaction fingerprints from sequence data

Interformer. Jupyter Notebook

boltz. Official repository for the Boltz biomolecular interaction models

ColabFold. Making Protein folding accessible to all!

localcolabfold. ColabFold on your local PC

AI2BMD. AI-powered ab initio biomolecular dynamics simulation

dplm. The Family of Diffusion Protein Language Models (DPLM)

datamapplot. Creating beautiful plots of data maps

AMPLIFY. Python

FLIP. A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

tape. Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

BioPhi. BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.

Umol. Protein-ligand structure prediction

esm-AxP-GDL. Python

EvolvePro. PLM based active learning model for protein engineering

CARE. CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes

AnnotationVocabulary. Jupyter Notebook

cheap-proteins. Joint embedding of protein sequence and structure with discrete and continuous compressions of protein folding model latent spaces. http://bit.ly/cheap-proteins

raygun. Template-based protein design with Raygun

CaLM. Protein language model trained on coding DNA

RiNALMo. RiboNucleic Acid (RNA) Language Model

RNA-FM. Nature Methods: RNA foundation model (together with RhoFold)

PSALM. Protein sequence domain annotation with a language model

protpardelle. Diffusion-based all-atom protein generative model.

Metabuli. Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

ProGen2-finetuning. Finetuning ProGen2 protein language model for generation of protein sequences from selected protein families.

esm. Jupyter Notebook

ECPICK. Python

spades. SPAdes Genome Assembler

phylophlan. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

Jellyfish. A fast multi-threaded k-mer counter

hostile. Precise host read removal

openff-forcefields. Force fields produced by the Open Force Field Initiative

openfe. The Open Free Energy toolkit

openff-toolkit. The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

gLM. Genomic language model predicts protein co-regulation and function

transformers. 🤗 Transformers: the model-definition framework for state-of-the-art machine learning models in text, vision, audio, and multimodal models, for both inference and training.

alphaflow. AlphaFold Meets Flow Matching for Generating Protein Ensembles

EvoProtGrad. Directed evolution of proteins in sequence space with gradients

pymbar. Python implementation of the multistate Bennett acceptance ratio (MBAR)

D-SCRIPT. A structure-aware interpretable deep learning model for sequence-based prediction of protein-protein interactions

foldseek. Foldseek enables fast and sensitive comparisons of large structure sets.

protein_scoring. Generating and scoring novel enzyme sequences with a variety of models and metrics

evo. Biological foundation modeling from molecular to genome scale

PLM_SWE. Implementation code for the paper "Aggregating Residue-Level Protein Language Model Embeddings with Optimal Transport"

e2eatp. A fast and high-accuracy protein-ATP binding residue prediction via protein language model

m-ionic. Protein-metal ion interaction modeling

hmmer3di. hmmer3 and easel patched to support the 3di alphabet.

ECRECer. Dual-core Multi-agent Learning Framework For EC Number Prediction

genome_portal_api. Python package to access and download data from the ATCC Genome Portal (https://genomes.atcc.org/)

megaDNA. Jupyter Notebook

AToM-OpenMM. OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method

yank. An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

LigandMPNN. Python

rf_diffusion_all_atom. Public RFDiffusionAA repo

RoseTTAFold-All-Atom. Python

bebi103. Utilities for BE/Bi 103

NFL2K5-Resurrected.

chiaki-ng. Next-Generation of Chiaki (the open-source remote play client for PlayStation)

Complete-Fire-Red-Upgrade. A complete upgrade for FireRed, including an upgraded Battle Engine.

genslm. GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics

polyply_1.0. Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

hyena-dna. Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

ByProt. Python

GeoDock. Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

ADCP. AutoDock CrankPep for peptide and disordered protein docking

scikit-optimize. Sequential model-based optimization with a `scipy.optimize` interface

pLM-BLAST. Detection of remote homology by comparison of protein language model representations

bopp. Black-box optimization of peptides and proteins

SaProt. Saprot: Protein Language Model with Structural Alphabet (AA+3Di)

ColossalAI. Making large AI models cheaper, faster and more accessible

openmmtools. A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

haddock3. Official repo of the modular BioExcel version of HADDOCK

making-it-rain. Cloud-based molecular simulations for everyone

simple-simulate-complex. Simple protein-ligand complex simulation with OpenMM

openmm. OpenMM is a toolkit for molecular simulation using high performance GPU code.

masif. MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

meld. Modeling with limited data

PeSTo. Geometric deep learning method to predict protein binding interfaces from a protein structure.

nucleotide-transformer. Foundation Models for Genomics & Transcriptomics

genie. De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds

evodiff. Generation of protein sequences and evolutionary alignments via discrete diffusion models

lightdock-rust. A Rust implementation of the LightDock macromolecular docking software

lightdock. Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

esmologs. Local homology search powered by ESM-2 language model, foldseek, hhsuite, and hmmer.

ThermoMPNN. GNN trained to predict changes in thermodynamic stability for protein point mutants

ProstT5. Bilingual Language Model for Protein Sequence and Structure

ThemePark. Fun ggplot themes for popular culture

MMseqs2. MMseqs2: ultra fast and sensitive search and clustering suite

murraylab_tools. Functions for building Echo picklists and directions for setting up source plates for the Echo. Mostly intended for setting up TX-TL experiments.

EpHod. Machine learning prediction of enzyme optimum pH

engineered-riboregulator-ML. Sequence-to-function deep learning frameworks for engineered riboregulators

CLEAN. CLEAN: a contrastive learning model for high-quality functional prediction of proteins

progen. Official release of the ProGen models

gnina. A deep learning framework for molecular docking

Ankh. Ankh: Optimized Protein Language Model

sleepwalk. Exploring dimension-reduced embeddings

pydock_tutorial. PyDock Tutorial

papers_for_protein_design_using_DL. List of papers about Proteins Design using Deep Learning

protein_generator. Joint sequence and structure generation with RoseTTAFold sequence space diffusion

openfold. Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

oddt. Open Drug Discovery Toolkit

excel-html. HTML

AutoGPT. AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.

DiffDock-PP. Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)

langchain. The agent engineering platform.

RFdiffusion. Code for running RFdiffusion

TemStaPro. TemStaPro - a program for protein thermostability prediction using sequence representations from a protein language model.

DiffDock. Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

peft. 🤗 PEFT: State-of-the-art Parameter-Efficient Fine-Tuning.

LoRA. Code for loralib, an implementation of "LoRA: Low-Rank Adaptation of Large Language Models"

activeSVC. Jupyter Notebook

repliclust. Natural Language-Based Synthetic Data Generation for Cluster Analysis.

diamond. Accelerated BLAST compatible local sequence aligner.

highdimensional-decision-boundary-plot. Estimating and plotting the decision boundary (decision surface) of machine learning classifiers in higher dimensions (scikit-learn compatible)

species-aware-DNA-LM. Species-aware DNA language modeling

iqplot. iqplot: Bokeh plots with one quantitative variable

gget. 🧬 gget enables efficient querying of genomic reference databases

Machine-learning-for-proteins. Listing of papers about machine learning for proteins.

seqkit. A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

protein_gibbs_sampler. Gibbs sampling for generating protein sequences

esm. Evolutionary Scale Modeling (esm): Pretrained language models for proteins

ColabDesign. Making Protein Design accessible to all via Google Colab!

protein-sequence-models. Python

bioCRNpyler. A modular compiler for biological chemical reaction networks