fluorescence tools

tttrlib

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)

chisurf

Global analysis platform for fluorescence data

LabelLib

Library for coarse-grained simulations of probes flexibly coupled to biomolecules.

FRETlines

fit2x

Maximum likelihood fits for low photon count data - For active develeopment visit gitlab.peulen.xyz

Olga

FRET-screening of conformations and experiment planning

PAM

This is a mirror of the PAM repository hosted on GitLab. Please refer to the GitLab repository for active development.

Seidel

Seidel software for FRET-nanoscopy analysis and automated TRACE-FRET analysis

Abberior-Tools

python scripts for Abberior microscope

avtraj

IMP.bff

IMP's Bayesian Fluorescence Framework

redRobin

redRobin software for CELFIS analysis

SAXS_score

Python script to fit and score theoretical ensemble-averaged SAXS profile against experimental SAXS data

1D_GaussianFit

Matlab script to fit univariate Gaussian Mixture Model (GMM) to a distribution of an observable

3D_DensityMap

Python script to compute 3D density map for an ensemble of conformational models

clsmview

CLSM viewer for ChiSurf

contact_map

Python script for mapping the presence of inter-residue contacts in a biomolecule

distogram

Python script for calculating ensemble weighted inter-residue distance histogram (distogram)

distogram_MuStd

Python script to compute and visualize residue pairwise mean distance and standard deviation of a distogram

flr2mmcif

Convert a spreadsheet with fluorescence information to a mmcif file for deposition in PDB-Dev

FourierShellCorr

Python script to compute Fourier Shell Correlation curve between two half-3D density maps

Hbond

Python script for identifying presence of hydrogen bonds based on geometrical criteria

k2dist

Compute and visualize orientation factor (kappa2) distributions

MaxEnt-pRda

Re-weighting of conformational ensembles towards the inter-dye distance distributions derived from experiment

ndxplorer

Histograms of multidimensional data

quest

QuEst - Quenching Estimator for fluorophores coupled to proteins - active development on gitlab.peulen.xyz

rmsd2D

Python script for pair-wise RMSD comparison between two ensembles of protein structures

RotCorrFun

Python script to compute rotational correlation function of a protein backbone N-H vector

SAXS_profile

Python script to compute theoretical ensemble-averaged SAXS profile for a biomolecule

tttrconvert

A simple converter for tttr files