branchialspace

branchialspace's Stars

• exelban/stats

  macOS system monitor in your menu bar

  Language:Swift26.9k1251.8k888

• KindXiaoming/pykan

  Kolmogorov Arnold Networks

  Language:Jupyter Notebook15.3k1124171.4k

• evo-design/evo

  Biological foundation modeling from molecular to genome scale

  Language:Jupyter Notebook1.2k2360150

• gcorso/DiffDock

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

  Language:Python1.1k18232272

• BradyAJohnston/MolecularNodes

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

  Language:Python9311933989

• gromacs/gromacs

  Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.

  Language:C++722720335

• hyattpd/Prodigal

  Prodigal Gene Prediction Software

  Language:C451269885

• MinkaiXu/GeoDiff

  Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

  Language:Python33863173

• tech-srl/how_attentive_are_gats

  Code for the paper "How Attentive are Graph Attention Networks?" (ICLR'2022)

  Language:Python31311836

• zrqiao/NeuralPLexer

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

  Language:Jupyter Notebook27565072

• steineggerlab/foldcomp

  Compressing protein structures effectively with torsion angles

  Language:C++16354414

• aqlaboratory/genie2

  Protein structure diffusion model for unconditional protein generation and motif scaffolding

  Language:Python1338920

• iRASPA/RASPA2

  Classical molecular simulation code

  Language:C13184483

• jasonkyuyim/multiflow

  Language:Python1253127

• Genentech/equifold

  Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

  Language:Python11810617

• Roestlab/massformer

  Tandem Mass Spectrum Prediction with Graph Transformers

  Language:Python768627

• Wangchentong/Proteus

  Pytorch implementation for ICML 2024 paper Proteus: Exploring Protein Structure Generation for Enhanced Designability and Efficiency.

  Language:Python72334

• Bitbol-Lab/ProtMamba-ssm

  ProtMamba: a homology-aware but alignment-free protein state space model

  Language:Jupyter Notebook52297

• timduignan/Scalable-Electrolyte-Simulation

  This repository contains the data and scripts necessary to reproduce the results presented in the paper: **"Scalable molecular simulation of electrolyte solutions with quantum chemical accuracy"** by Junji Zhang, Joshua Pagotto, Tim Gould, and Timothy T. Duignan.

  Language:Jupyter Notebook39402

• Iolo-Jones/DiffusionGeometry

  The code for "Diffusion Geometry" (2024).

  Language:Jupyter Notebook38204

• JonathanGorard/Categorica

  Categorica: a pure and applied category theory framework for the Wolfram Language

  Language:Mathematica28633

• Blackzxy/LoGAH

  Language:Python21241

• joey00072/Attention-as-graph

  alternative way to calculating self attention

  Language:Python18302

• divelab/MFA

  Official code repository of paper Equivariance via Minimal Frame Averaging for More Symmetries and Efficiency.

  Language:Jupyter Notebook16200

• JonathanGorard/Cosmos

  The Cosmos numerical relativity code (with unstructured AMR)

  Language:C++16101

• UCLOrengoGroup/cath-alphaflow

  Language:Python164261

• Multiscale-Modelling-of-Complex-Systems/Native-contacts-determination-from-MD

  We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU approach (http://pomalab.ippt.pan.pl/GoContactMap/).

  Language:Tcl15001

• psipred/ted-tools

  ML toolset for creating TED: The Encyclopedia of Domains

  Language:Python10311

• KIT-Workflows/PCU-MOF

  PCU-MOF

  Language:Python4201

• UCLOrengoGroup/ted-web

  TED: Automated Domain Parsing of AlphaFold DB

  Language:TypeScript32250