biochemistry

There are 145 repositories under biochemistry topic.

  • EMDA

    Python package for easy analysis of MD simulations based on MDAnalysis.

    Language:Jupyter Notebook3

  • process-rate-estimator

    A GitHub repository for the process rate estimator developed for the Sustainable Agroecosystems Group at ETH.

    Language:R3

  • autodock-vina-automator

    A script to run docking experiments in AutoDock Vina for several ligands at once with technical replicates.

    Language:Python3

  • prodivis

    A tool to accurately normalize and visualize protein distribution in 3D structures imaged with confocal microscopy using z-stacks.

    Language:Python3

  • SACMES

    Software for the Analysis and Continuous Monitoring of Electrochemical Systems.

    Language:Python3

  • julia-curve-fitting

    Pluto notebook for curve fitting

    Language:Julia3

  • HADDOCKer

    Docker images for the running the HADDOCK system for predicting the structure of biomolecular complexes.

    Language:Shell3

  • webchemvr

    WebVR implementation of molecular structure viewer NGL

    Language:JavaScript3

  • Drugbank-Classification

    Drugbank Classification

    Language:Jupyter Notebook3

  • LANS

    A MATLAB-based program for processing and analysis of nanoSIMS data

    Language:MATLAB3

  • BioMight

    BioMight - Human Biological Animation Engine

    Language:Java3

  • tuilab.github.io

    Tui Lab – Bioinformatics resources, scripts and ideas.

    Language:HTML3

  • moulinette

    Bioinformatics (biochemistry) data processing scripts for NMR, and protein data analysis (PyMOL)

    Language:Python3

  • AR-Structural-Biology

    Augmented Reality object for biochemistry

    Language:HTML2

  • Burn_your_fat

    Biochemistry DIY board game

    2

  • blog

    My personal blog!

    Language:XSLT2
  • Non-Equilibrium-Toolbox

    Non-Equilibrium-Toolbox

    Toolkit for quantifying errors in non-equilibrium data

    Language:Python2
  • Step-Detection-Algorithm

    Step-Detection-Algorithm

    Tool for detecting abrupt step changes in noisy signals

    Language:Python2

  • biochemr

    Tools For User-Friendly & Reproducible Analysis of Biochemistry Experiments

    Language:R2

  • MolecularFaces

    Java Server Faces UI components for chemistry and biochemistry

    Language:Java2

  • AutoDockVina-BatchSubmission

    A simple batch submission script to submit jobs to AutoDock Vina on Linux and MacOS developed by Bhavesh Ashok.

    Language:Shell2
  • clampSegGUI

    clampSegGUI

    Graphical user interface allows easy access to the multiscale model-free idealization methods in the R-package clampSeg (https://cran.r-project.org/package=clampSeg). It supports the model-free segmentation methods JSMURF (https://ieeexplore.ieee.org/document/6655999), JULES (https://ieeexplore.ieee.org/document/8374882) and HILDE (https://arxiv.org/abs/2008.02658). These methods combine multiscale testing with deconvolution to idealise patch clamp recordings. They allow to deal with subconductance states and flickering.

    Language:Python2

  • model_reduction

    Matlab implementation of automated model reduction of biochemical reaction networks

    Language:MATLAB2

  • helixvis

    Visualize alpha-helical peptide sequences in R using helical wheels and wenxiang diagrams. See https://doi.org/10.21105/joss.01008 for more details.

    Language:R2

  • ABC-Laboratory

    ABC-Laboratory is a prototypical simulation software calculating the fluorescence or absorption of different 'biomolecules'. It uses the Godot Game Engive (v.3) and is the result of my Bachelor Hands-on / internship.

    Language:GDScript2

  • rfret

    Analyze FRET Binding Data with R

    Language:R2

  • JBioFramework

    Growing suite of proteomics simulations for educational purposes

    Language:Java2

  • ypkpathway

    Automatic pathway assembly with the YeastPathwayKit

    Language:Python2

  • Drug-Discovery-with-Python-and-Machine-Learning

    Explore data collection, analysis, and machine learning for drug discovery. Create predictive models, perform EDA, and deploy as web apps.

    1

  • Extrator-de-Parametros-Analise-Hemograma-e-Bioquimico

    Software em Python para varrer arquivos PDF e extrair parâmetros diretamente para arquivo Excel

    Language:Python1

  • tape

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

    Language:Shell1

  • dude

    A database database of useful decoys designed to help benchmark molecular docking programs by providing challenging decoys with protein-ligand binding affinities

    Language:Dockerfile1

  • molecule-language-models

    Transformer models for generative modeling of bioactive chemical small molecules

    Language:Jupyter Notebook1

  • orca-intro

    The introduction and molecules with ORCA software.

    1

  • ElixirSeeker-ElixirFP

    A robust Python library designed for the generation and optimization of molecular fingerprints

    Language:Python1

  • biofidelicx-quizzard

    biofidelicX quizzard is the ideal place to start if you're studying for an exam, trying to increase your knowledge of bio-science, or just seeking for a fun and engaging method to learn.

    Language:JavaScript1