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    77 repositories

    • miniomm

      Public
      A simple OpenMM wrapper for common-case MD runs
      simulationopenmmopenmm-wrapper
      Python
      •3•4•1•0•Updated Jan 24, 2025Jan 24, 2025

    • DTW-G-Cubed

      Public
      The repository contains the R scripts for the DTW calculations performed and presented for the G-Cubed paper on the methodology of DTW custom technique.
      R
      •
      Creative Commons Attribution 4.0 International
      •2•0•0•0•Updated Dec 28, 2024Dec 28, 2024

    • DL4Proteins-notebooks

      Public
      Colab Notebooks covering deep learning tools for biomolecular structure prediction and design
      Jupyter Notebook
      •44•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • fpocket

      Public
      fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. [..]
      C
      •
      MIT License
      •64•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • Structural-Bioinformatics

      Public
      This repository includes the slides and the practicals for the course of Structural Bioinformatics of the MBB/QB degrees at the University of Milano, originally inspired by https://github.com/pb3lab/ibm3202
      Jupyter Notebook
      •
      MIT License
      •10•1•0•0•Updated Dec 5, 2024Dec 5, 2024

    • ZernikeMoments

      Public
      Fork of '3D Zernike Descriptors' library from 3d research Uni-Bonn
      C++
      •11•0•0•0•Updated Nov 24, 2024Nov 24, 2024

    • biostructure

      Public
      PLpgSQL
      •
      Apache License 2.0
      •1•0•0•0•Updated Nov 20, 2024Nov 20, 2024

    • moleculekit

      Public
      MoleculeKit: Your favorite molecule manipulation kit
      Python
      •
      Other
      •38•1•0•0•Updated Nov 19, 2024Nov 19, 2024

    • plumed2-pycv

      Public
      PYCV module for PLUMED2. See the src/pycv directory.
      C++
      •
      GNU Lesser General Public License v3.0
      •295•8•1•0•Updated Nov 19, 2024Nov 19, 2024

    • mdCATH

      Public
      This repository houses all the scripts and notebooks utilized for generating, analyzing, and validating the mdCATH dataset. Some user examples are also available.
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • Chen_BiophysJ_2009

      Public
      A number of implementations of Chen-Wang-Sherman's (Biophys J 2008) model of insulin secretion
      MATLAB
      •0•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • mdcath-utils

      Public archive
      0•1•0•0•Updated Sep 6, 2024Sep 6, 2024

    • bruno_labtools

      Public
      Python
      •1•0•0•0•Updated Aug 1, 2024Aug 1, 2024

    • ecl2

      Public
      ECL2 clustering interactive table and app
      R
      •0•0•0•0•Updated Jun 13, 2024Jun 13, 2024

    • 2024-MolSim-UniPD

      Public
      Material for the Molecular Simulations module (Prof. Fuxreiter)
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•1•0•0•Updated May 17, 2024May 17, 2024

    • MD-Tutorial-Data

      Public
      Data for various MD analysis tutorials
      Jupyter Notebook
      •0•1•0•0•Updated May 6, 2024May 6, 2024

    • openmm-cookbook

      Public
      Proof-of-concept for the OpenMM Cookbook
      Jupyter Notebook
      •10•0•0•0•Updated Apr 3, 2024Apr 3, 2024

    • beta-arrestin1-sca

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 6, 2024Mar 6, 2024

    • Hidalgo

      Public
      find clusters of different intrinsic dimension
      C++
      •8•0•0•0•Updated Feb 29, 2024Feb 29, 2024

    • 2024-Markov-Tutorial-BCN

      Public
      Markov Seminar for prof. Selent's course
      0•0•0•0•Updated Jan 31, 2024Jan 31, 2024

    • 2024-GSN-Tutorial-BCN

      Public
      For Prof. Selent's course
      Jupyter Notebook
      •0•0•0•0•Updated Jan 30, 2024Jan 30, 2024

    • 2023-Markov-Tutorial-UniMi

      Public
      Markov Seminar for prof. Camilloni's course
      0•0•0•0•Updated Nov 9, 2023Nov 9, 2023

    • MLCE

      Public
      Python
      •2•0•0•0•Updated Jul 24, 2023Jul 24, 2023

    • ACEMD-PLUMED

      Public archive
      Running biased simulations with PLUMED and ACEMD
      Gnuplot
      •2•2•0•0•Updated May 29, 2023May 29, 2023

    • 2023-OpenMM-MD-UniPD

      Public
      For prof. Fuxreiter's Course
      0•1•0•0•Updated May 15, 2023May 15, 2023

    • vmd_density_profile

      Public
      Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD.
      Tcl
      •13•36•2•0•Updated May 8, 2023May 8, 2023

    • 2023-Markov-Tutorial-BCN

      Public
      Markov Tutorial for 2023 MSI
      Jupyter Notebook
      •0•0•0•0•Updated May 1, 2023May 1, 2023

    • 2023-GSN-Tutorial-BCN

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 27, 2023Apr 27, 2023

    • ProteinBERT_HL

      Public
      Milad's thesis code: peptide hemolytic activity predictor
      Jupyter Notebook
      •2•0•0•0•Updated Apr 16, 2023Apr 16, 2023

    • biozernike

      Public
      Protein structure descriptors and alignment based on 3D Zernike moments.
      Java
      •
      MIT License
      •12•0•0•0•Updated Apr 13, 2023Apr 13, 2023