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The lab has a long track record of building web servers and software for protein structure prediction, membrane protein topology, and quality assessment.

Selected prediction resources

TOPCONS

Consensus topology prediction for membrane proteins.

TOPCONS-single

Fast membrane protein topology prediction from a single sequence.

Pcons.net

Consensus protein structure prediction and modelling.

TOBMODEL

Automatic modelling of beta-barrel membrane proteins.

ABAG-rank

Ranking AlphaFold models of Antibody-Antigen complexes.

Public repositories from lab members

Automatically fetched from public GitHub and GitLab profiles configured in data/site.yaml.

GitHub

https://github.com/ElofssonLab · 47 public repositories

Showing 10 of 47 repositories.

Sarah Narrowe Danielsson

PhD student

@SarahND97 · 10 public repositories

  • alphafold-homodimers
  • SPOC
    Code repository for the SPOC tool for scoring binary AF-M predicitons.
  • alphafold
    Open source code for AlphaFold.
  • alphaflow
    AlphaFold Meets Flow Matching for Generating Protein Ensembles
  • ML_medbioinfo
    Machine Learning in Medical Bioinformatics
  • esm
    Evolutionary Scale Modeling (esm): Pretrained language models for proteins
  • MedBioinfo
    MedBioinfo course material
  • D-SCRIPT
    A structure-aware interpretable deep learning model for sequence-based prediction of protein-protein interactions
  • scvi-tools
    Deep probabilistic analysis of single-cell omics data
  • react_project

Matteo Tadiello

PhD student

@tadteo · 59 public repositories

  • ABAG-Rank
  • tadteo.github.io
  • bioinfo_DeepLearningLabs
    Deep Learning Labs for the Bioinformatics course
  • cool-effects
    A repo for cool visual effects for videos (more for art and for fun)
  • antibody-antigen-predictions-ranker
  • DockQ
    DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models
  • BT_eventb
    An Event-b formalization of Behavior tree
  • boltz
    Official repository for the Boltz biomolecular interaction models
  • Progetto_WEB_2018
  • flow_matching
    A PyTorch library for implementing flow matching algorithms, featuring continuous and discrete flow matching implementations. It includes practical examples for both text and image modalities.
  • secondary_structure_predictor_project
    A secondary structure predictor project for a bioinformatic university course
  • Open3D
    Open3D: A Modern Library for 3D Data Processing
  • openfold
    Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
  • openfold-large-proteins
  • FLEX-BEATS
    Flexible Biomolecule Encoding through Adaptive Tokenizetion of Sequences
  • protein_ensembles
  • Uni-Fold
    An open-source platform for developing protein models beyond AlphaFold.
  • drones_gazebo
    Collision avoidance implementation for autonomous drones
  • alphafold
    Open source code for AlphaFold.
  • numpy
    The fundamental package for scientific computing with Python.
  • game_of_life
    A python implementation of the game of life (just for fun)
  • yolov7
    Implementation of paper - YOLOv7: Trainable bag-of-freebies sets new state-of-the-art for real-time object detectors
  • STL-AEP
    Guiding Efficient 3D Exploration with Temporal Logic
  • CNN
    A simple CNN
  • gitignore
    A collection of useful .gitignore templates
  • serverless-full-stack-apps-azure-sql
    Full stack solution using Javascript, Azure Static Web Apps, Azure Function, Azure SQL Database and a microservice architecture to monitor in real-time public transportation data, create a geofence and send notification when geofence is activated
  • wasp_SE_course
    Resources and student assignments for the WASP Software Engineering course
  • turtlebot_exploration
  • WASP_AI_Course_Module3
    Atrial fibrillation classification from the ECG . Assignment for the WASP Course "Artificial Intelligence and Machine Learning"
  • WASP_AI_Course_Module2
  • WASP_AI_Course2022
    Repo for assignments of the course WASP Artificial Intelligence and Machine Learning 2022
  • Safe-RL-2
    Implementation for Safe RL using ray and rllib framework
  • Safe-RL
    State driven safety for reinforcement learning without reward
  • QC_simulator
    A simulation of a quantum computer
  • pytorch_tutorial
    A pytorch tutorial and example. Mainly based on this [video](https://www.youtube.com/watch?v=c36lUUr864M&t=5297s)
  • tensorflow-yolov4-tflite
    YOLOv4, YOLOv4-tiny, YOLOv3, YOLOv3-tiny Implemented in Tensorflow 2.0, Android. Convert YOLO v4 .weights tensorflow, tensorrt and tflite
  • nnn
    Work in progress for general purpose neural networks that allows cyclic graphs
  • .emacs.d
    My Emacs configuration files repo
  • image_recognition
    Test of various image recognition techniques with a focus on thermal images
  • jetson-gpio
    A Python library that enables the use of Jetson's GPIOs
  • bigspring-hugo-startup-theme
  • gym-gazebo
    Refer to https://github.com/AcutronicRobotics/gym-gazebo2 for the new version
  • hugo-theme-sam
    A Simple and Minimalist theme for Hugo with a focus on typography and content.
  • map_pcl
    Simple map from point cloud with pcl
  • simple_movement
    simple moviment for 3d object in gazebo
  • RL_AEP_ws
    The main project repo for RL_AEP
  • simple_uav_gazebo
    A simple UAV Gazebo integration
  • rl_aep
    Reinforcement Learning project for autonomous exploration with drones based on AEP explortion method (https://github.com/danielduberg/STL-AEP)
  • octomap_mapping
    ROS stack for mapping with OctoMap, contains octomap_server package
  • DAIIA-project
  • RL_lab1
    Reinforcement learning exercises for the course EL2805HT191 at KTH
  • festival_simulation
    Festival simulations for the course Distributed Artificial Intelligence and Intelligent Agents
  • Firmware
    PX4 Pro Autopilot Software
  • DSMA
  • ProjectDeepLearning
    Project for a Deep Learning course starting from the code of Composer https://github.com/HackerPoet/Composer
  • collision_avoidance
  • tesi_laurea_latex
    Tesi di laurea triennale in informatica aa: 2017/2018
  • examware
  • Tadiello-se2jan26