Simon Duerr

dEVA. design by evolutionary algorithm

marimo. A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. Stored as pure Python. All in a modern, AI-native editor.

gimie. Extract linked metadata from repositories

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

boltz. Official repository for the Boltz biomolecular interaction models

BindCraft. User friendly and accurate binder design pipeline

molstar. A comprehensive macromolecular library

torch_pgn. Proximity Graph Networks

NSGA-II. Implementation of NSGA-II algorithm in form of a python library.

pytorch-multi-class-focal-loss. An (unofficial) implementation of Focal Loss, as described in the RetinaNet paper, generalized to the multi-class case.

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

extract-line-chart-data. Software that extracts line chart data from images.

alphafold3-pytorch. Implementation of Alphafold 3 from Google Deepmind in Pytorch

sequence-viewers. TypeScript

spyrmsd. 📐 Symmetry-corrected RMSD in Python

MetalHawk. A machine learning-based approach for classifying metal site geometry.

progres. Fast protein structure searching or your money back

ScientificFigures. A comprehensive guide on how to create beautiful scientific figures for technical publications, presentations, and posters

molstar-svelte. Svelte components wrapping the Mol* toolkit.

rosetta. The Rosetta Bio-macromolecule modeling package. Available through license with the University of Washington.

multiflow. Python

NeuralPLexer. NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

PinMyMetal. PinMyMetal: Accurately model metal binding sites through a hybrid learning system

LigandDiff. LigandDiff

healthicons. A collection of open source icons for public health projects.

LigandMPNN. Python

Frame2seq. Structure-conditioned masked language modeling for protein sequence design

vtracer. Raster to Vector Graphics Converter

ProteinFlow. Versatile computational pipeline for processing protein structure data for deep learning applications.

chroma. A generative model for programmable protein design

Master-of-metals. Tool for the prediction of metal binding sites in protein structures

bioicons. A library of free open source icons for science illustrations in biology and chemistry

FoldFlow. FoldFlow: SE(3)-Stochastic Flow Matching for Protein Backbone Generation

3Dmol.js. WebGL accelerated JavaScript molecular graphics library

DiffAffinity. Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model (NeurIPS 2023 Poster)

RockPdf. PHP

RFdiffusion. Code for running RFdiffusion

tldraw. Build infinite canvas apps in React with the tldraw SDK. World's best, top-most agent recommended #1 five star SDK.

tmol. TMol

immich. High performance self-hosted photo and video management solution.

RoseTTAFold2. Python

protpardelle. Python

xyztransformer. coming soon

ammonia. Repair and secure untrusted HTML

svg2xml. SVG to XML mxGraph stencil definition translation tool

svgedit. Powerful SVG-Editor for your browser

github-action-utils. Collection of python functions that can be used to run GitHub Action Workflow Commands

DiffusionProteinLigand. Python

SVD-of-MSAs. This repository contains a set of scripts for performing singular value decomposition on protein multiple sequence alignments, and analyzing the results.

e3_diffusion_for_molecules. Python

DiffSBDD. A Euclidean diffusion model for structure-based drug design.

DiffLinker. DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design

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

RoseTTAFold2NA. RoseTTAFold2 protein/nucleic acid complex prediction

design_tools. A compilation of deep learning methods for protein design

ColabFold. Making Protein folding accessible to all!

metal-site-prediction. Jupyter Notebook

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

ATOMRefine. 3D equivariant graph transformer for all-atom refinement of protein tertiary structures

rcsb-saguaro. 1D Feature Viewer

postleitzahlen. Postleitzahlengebiete in Deutschland / German Postcode Areas

timed-design. Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis

echem. eChem: Jupyter book on theoretical chemistry

DeltaDihedral. Calculate delta dihedrals as in figure 1 of "A genetically encoded, high-signal-to-noise maltose sensor" Marvin et al 2011.

MolecularNodes. Toolbox for molecular animations in Blender, powered by Geometry Nodes.

progen. Official release of the ProGen models

perovskites-distortions. Collection of useful functions to manipulate/analyse the structures of hybrid organic-inorganic perovskites

tmtools. Python bindings for the TM-align algorithm and code for protein structure comparison developed by Zhang et al.

af_backprop. Python

ProteinMPNN. Code for the ProteinMPNN paper

yeger. Monorepo for @yeger/ NPM packages

contentv2-nuxt3. Simple site created with the new content v2 for nuxt 3

ScanNet. Python

protein-sequence-models. Python

pyscript. An open source platform for Python in the browser. https://pyscript.net Docs: https://docs.pyscript.net/ Try it: https://pyscript.com/ Community: https://discord.gg/HxvBtukrg2

funnel_maker. Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.

atomium. Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)

coot. Software for macromolecular model-building

PeptideBuilder. A simple Python library to generate model peptides

pyMUT. Python

memray. Memray is a memory profiler for Python

dMaSIF. Jupyter Notebook

aposteriori. DNN based protein design.

gnina-torch. 🔥 PyTorch implementation of GNINA scoring function for molecular docking

SciCompforChemists. Scientific Computing for Chemists with Python is a free book for teaching basic coding skills to chemists using Python, Jupyter notebooks, and the other Python software. This textbook teaches a variety of Python packages including NumPy, SciPy, matplotlib, pandas, seaborn, nmrglue, SymPy, scikit-image, scikit-learn, and others.

htmd. HTMD: Programming Environment for Molecular Discovery

nordigen-python. A Python client library for interacting with GoCardless (was Nordigen) banking API which allows access to 100's of banks across Europe

processwire. ProcessWire 3.x is a friendly and powerful open source CMS with a strong API.

black. The uncompromising Python code formatter

EquiBind. EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

EquivariantMultipoleGNN. Equivariant GNN for the prediction of atomic multipoles up to quadrupoles.

moleculekit. MoleculeKit: Your favorite molecule manipulation kit

ZincBindPredict. Predictive models of zinc binding

torchdrug. A powerful and flexible machine learning platform for drug discovery

biometall. BioMetAll is a command line application to allow the identification of metal-binding sites in proteins from backbone preorganization.

deeprank. This repository has been integrated in https://github.com/DeepRank/deeprank2

Deeprank-GNN. Graph Network for protein-protein interface

dqc. Differentiable Quantum Chemistry (only Differentiable Density Functional Theory and Hartree Fock at the moment)

invariant-point-attention. Implementation of Invariant Point Attention, used for coordinate refinement in the structure module of Alphafold2, as a standalone Pytorch module

egnn. Python

MAHOMES. Metal Activity Heuristic of Metalloprotein and Enzymatic Sites (MAHOMES) - Predicts if a protein bound metal ion is enzymatic or non-enzymatic

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

CNN_protein_landscape. R

pyvista. 3D visualization and mesh analysis for science and engineering

palmerpenguins. A great intro dataset for data exploration & visualization (alternative to iris).

fosschemistry. Computational chemistry with free and open source software

QUICK. QUICK: A GPU-enabled ab intio quantum chemistry software package

cgdms. Differentiable molecular simulation of proteins with a coarse-grained potential

pyfoldx. pyFoldX: python bindings for FoldX.

rootstock. Clone me to create your Manubot manuscript

gnina. A deep learning framework for molecular docking

chem1000. Jupyter Noteboks for lecture and assignments for CHEM 1000: Mathematics for Chemistry at University of Pittsburgh

nequip. NequIP is a code for building E(3)-equivariant interatomic potentials

gh-action-repo-selective-sync. Automatically synchronize target from source repos by specifying what to copy

alphafold. Open source code for AlphaFold 2.

papers. Material from papers from KULL centre

Fluency-Translation. A DeepL translation integration for the ProcessWire CMF/CMS platform

csa-admin. Web application to manage CSA (Community Supported Agriculture), ACP (Agriculture Contractuelle de Proximité) or Solawi (Solidarische Landwirtschaft) organizations.

protein_seq_des. Code for our paper "Protein sequence design with a learned potential"

protein_seq_des. Code for our paper "Protein sequence design with a learned potential"

DLPacker. DLPacker

qm-tools. MolSSI Quantum Mechanics Tools workshop

psi4. Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

IEConv_proteins. Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures

morfeus. A Python package for calculating molecular features

academicons. An icon font for academics

icons. R package to easily insert web icons to RMarkdown

BioHackaton2021. Copenhagen Bioinformatics Hackathon 2021: Protein Edition

bio_embeddings. Get protein embeddings from protein sequences

v-craft. 🎨 A Toolset for Building Extensible Page Builders with Vue.js

heroicons.dev. Web viewer for Heroicons (V2 and V1)

svgo-addViewBox. svgo plugin which replaces width, height attributes of an svg with viewBox attribute to make it responsive.

orcid-php-client. php client to send and read workflows on orcid

libmolgrid. Comprehensive library for fast, GPU accelerated molecular gridding for deep learning workflows

condacolab. Install Conda and friends on Google Colab, easily

gromax. Python

Toy-MD. Python code for learning Molecular Dynamics simulations

thebe. Turn static HTML pages into live documents with Jupyter kernels.

basic_simulation_training. A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some training itself and linking out to other helpful information elsewhere. The intent is that this provide information on the prerequisites which will be required for understanding/following many of the other "best practices" documents being prepared.

pdb-tools. A dependency-free cross-platform swiss army knife for PDB files.

db-enzymes. Database of reaction barriers in proteins with structures

gaudi. GaudiMM: A modular optimization platform for molecular design

deap. Distributed Evolutionary Algorithms in Python

models. Trained caffe models

Combs. Convergent motifs for binding sites

graphein. Protein Graph Library

frustratometeR. R

ThermoNet. ThermoNet is a computational method for quantitative prediction of the impact of single-point mutations on protein thermodynamic stability. The core algorithm of ThermoNet is an ensemble of deep 3D convolutional neural networks.

seaborn. Statistical data visualization in Python

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

orcidProfile. A plugin to pull ORCID information into a PKP user profile

DeeplyTough. DeeplyTough: Learning Structural Comparison of Protein Binding Sites

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

Mini-Conf. Run a conference from your backyard.

chemrxiv-dashboard.github.io. Webpage for the ChemRxiv dashboard

SubscribeToMailchimp. Lightweight module for ProcessWire that lets you subscribe, update, unsubscribe and delete a user to a mailchimp list.

jax-unirep. Reimplementation of the UniRep protein featurization model.

Interactive_Tools. Interactive Tools for Machine Learning, Deep Learning and Math

vue-taggable-select. A multiple taggable select autocomplete dropdown component for Vue

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

UniRep. UniRep model, usage, and examples.

protherm-conversion. Convert and deposit ProTherm data into ProtaBank studies

mathematicalpython. Introduction to Mathematical Computing with Python and Jupyter

NCIPLOT-4.2. Program for revealing non-covalent interactions

nciplot. Program for revealing non-covalent interactions

secondary-fixed-navigation. A secondary navigation intended for users who want a quick overview of the page content, and be able to easily move from one section of the page to the other.

rgroup-pie. PoC code to generate a structure depictions with partial pie charts centered on R group atoms

terminal. The new Windows Terminal and the original Windows console host, all in the same place!

stackedit. In-browser Markdown editor

junest. The lightweight Arch Linux based distro that runs, without root privileges, on top of any other Linux distro.

qmmm-workshop. A repository containing the build steps for the ccpbiosim workshop on QM/MM

mol. Render ball-and-stick models of molecules.

rmsd. Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format