fluorescence tools

All

38 repositories

flr2mmcif
Public
Convert a spreadsheet with fluorescence information to a mmcif file for deposition in PDB-Dev
Python
•
MIT License
•1•0•0•0•Updated Oct 2, 2024Oct 2, 2024
tttrlib
Public
File format agnostic low level, high performance API to read and process time-tagged-time resolved (TTTR) data for single-molecule and image spectroscopy (Sample data: https://gitlab.peulen.xyz/skf/tttr-data)
python single-molecule fluorescence imaging fluorescence-microscopy-imaging ptu flim becker fluorescence-correlation picoquant
C++
•
BSD 3-Clause "New" or "Revised" License
•0•19•3•0•Updated Sep 30, 2024Sep 30, 2024
chisurf
Public
Global analysis platform for fluorescence data
correlation protein fluorescence spectroscopy multiple-datasets fluorescence-data global-analysis fluorescence-decays-analysis
Python
•
GNU General Public License v2.0
•1•13•14•0•Updated Sep 25, 2024Sep 25, 2024
IMP.bff
Public
IMP's Bayesian Fluorescence Framework
spectroscopy integrative-modeling
C++
•
GNU Lesser General Public License v2.1
•0•1•0•0•Updated Apr 18, 2024Apr 18, 2024
ndxplorer
Public
Histograms of multidimensional data
Python
•
GNU General Public License v2.0
•0•0•0•0•Updated Apr 1, 2024Apr 1, 2024
clsmview
Public
CLSM viewer for ChiSurf
Python
•
GNU General Public License v2.0
•0•0•0•0•Updated Mar 25, 2024Mar 25, 2024
k2dist
Public
Compute and visualize orientation factor (kappa2) distributions
Python
•
GNU General Public License v2.0
•0•0•0•0•Updated Mar 25, 2024Mar 25, 2024
tttrconvert
Public
A simple converter for tttr files
Python
•
GNU General Public License v2.0
•0•0•0•0•Updated Feb 17, 2024Feb 17, 2024
fit2x
Public
Maximum likelihood fits for low photon count data - For active develeopment visit gitlab.peulen.xyz
single-molecule fluorescence lifetime mle-estimation mle flim lifetime-analysis
C++
•
Mozilla Public License 2.0
•0•3•0•0•Updated Feb 12, 2024Feb 12, 2024
SAXS_score
Public
Python script to fit and score theoretical ensemble-averaged SAXS profile against experimental SAXS data
Python
•
Mozilla Public License 2.0
•1•1•0•0•Updated Sep 19, 2023Sep 19, 2023
FourierShellCorr
Public
Python script to compute Fourier Shell Correlation curve between two half-3D density maps
Python
•
Mozilla Public License 2.0
•1•0•0•0•Updated Sep 19, 2023Sep 19, 2023
distogram_MuStd
Public
Python script to compute and visualize residue pairwise mean distance and standard deviation of a distogram
Python
•
Mozilla Public License 2.0
•1•0•0•0•Updated Sep 19, 2023Sep 19, 2023
Hbond
Public
Python script for identifying presence of hydrogen bonds based on geometrical criteria
Python
•
Mozilla Public License 2.0
•1•0•0•0•Updated Sep 17, 2023Sep 17, 2023
3D_DensityMap
Public
Python script to compute 3D density map for an ensemble of conformational models
Python
•
Mozilla Public License 2.0
•1•0•0•0•Updated Sep 17, 2023Sep 17, 2023
distogram
Public
Python script for calculating ensemble weighted inter-residue distance histogram (distogram)
Python
•
Mozilla Public License 2.0
•1•0•0•0•Updated Sep 15, 2023Sep 15, 2023
rmsd2D
Public
Python script for pair-wise RMSD comparison between two ensembles of protein structures
Python
•
Mozilla Public License 2.0
•1•0•0•0•Updated Sep 15, 2023Sep 15, 2023
RotCorrFun
Public
Python script to compute rotational correlation function of a protein backbone N-H vector
Python
•
Mozilla Public License 2.0
•1•0•0•0•Updated Sep 14, 2023Sep 14, 2023
1D_GaussianFit
Public
Matlab script to fit univariate Gaussian Mixture Model (GMM) to a distribution of an observable
MATLAB
•
Mozilla Public License 2.0
•1•0•0•0•Updated Sep 14, 2023Sep 14, 2023
contact_map
Public
Python script for mapping the presence of inter-residue contacts in a biomolecule
Python
•
Mozilla Public License 2.0
•1•0•0•0•Updated Sep 14, 2023Sep 14, 2023
SAXS_profile
Public
Python script to compute theoretical ensemble-averaged SAXS profile for a biomolecule
Python
•
Mozilla Public License 2.0
•1•0•0•0•Updated Sep 14, 2023Sep 14, 2023
Seidel
Public
Seidel software for FRET-nanoscopy analysis and automated TRACE-FRET analysis
Jupyter Notebook
•
Mozilla Public License 2.0
•0•2•0•0•Updated Aug 30, 2023Aug 30, 2023
redRobin
Public
redRobin software for CELFIS analysis
Jupyter Notebook
•
Mozilla Public License 2.0
•0•1•0•0•Updated Aug 22, 2023Aug 22, 2023
Abberior-Tools
Public
python scripts for Abberior microscope
Python
•
Mozilla Public License 2.0
•0•1•0•0•Updated Sep 26, 2022Sep 26, 2022
quest
Public
QuEst - Quenching Estimator for fluorophores coupled to proteins - active development on gitlab.peulen.xyz
simulation fluorescence fret quenching dyes
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated May 31, 2022May 31, 2022
avtraj
Public
fluorescence fps simulation avs accessible-volumes md-trajectory
Python
•
GNU Lesser General Public License v2.1
•0•1•1•1•Updated Feb 9, 2022Feb 9, 2022
PAM
Public
This is a mirror of the PAM repository hosted on GitLab. Please refer to the GitLab repository for active development.
MATLAB
•
GNU General Public License v3.0
•0•3•1•0•Updated Aug 12, 2021Aug 12, 2021
FRETlines
Public
Jupyter Notebook
•
GNU General Public License v3.0
•0•4•0•0•Updated Aug 2, 2021Aug 2, 2021
Olga
Public
FRET-screening of conformations and experiment planning
fluorescence molecules fret conformations
C++
•
GNU General Public License v3.0
•1•3•9•0•Updated May 5, 2021May 5, 2021
MaxEnt-pRda
Public
Re-weighting of conformational ensembles towards the inter-dye distance distributions derived from experiment
Python
•
Mozilla Public License 2.0
•1•0•0•0•Updated Apr 28, 2021Apr 28, 2021
LabelLib
Public
Library for coarse-grained simulations of probes flexibly coupled to biomolecules.
fluorescence simulation-toolkit fret science-research pymol accessible-volumes
C++
•
Mozilla Public License 2.0
•3•9•3•1•Updated Mar 8, 2021Mar 8, 2021