May 4, 2024 · Protein residue–residue distance maps are used for remote homology detection, protein information estimation, and protein structure research.

A Python pipeline for protein sequence alignment and phylogenetic analysis using Biopython and Clustal Omega. Includes distance matrix calculation, UPGMA & NJ tree construction, custom node labeling, and enhanced tree visualizations. Outputs aligned sequences, trees in Newick format, and styled images.

Use setup_fasta.py to configure DeepDist to take a fasta sequence as input to predict distance map. setup_fasta.py requires downloading a package of about 580 GB. We recommend running setup_msa.py due to the smaller space requirements but you will need to …

Aug 7, 2020 · Our real-valued distance prediction method (PDNET-Distance), trained by reciprocating the distance maps, helps the deep learning optimization focus on correctly predicting shorter distances...

A custom Python script was used to map all identified peptides to sequence of protein of interest. Cleavage site to centroid distance (CSCD) was computed by the average Euclidean distance of all cleavage residues to the geometric center of protein as follows:

Nov 27, 2023 · protPy is a Python software package for generating a variety of useful physicochemical, biochemical and structural descriptors for protein sequences. All of these descriptors are calculated...

Oct 31, 2008 · We developed PConPy, an open-source Python module for generating contact maps, distance maps and HB-plots in a number of vector and raster image formats. Our aim was to provide an extensible tool for protein researchers to generate 2D protein maps for use in publication or structural analysis.

Go to the directory, use the following command to run predictions: python -W ignore make_predictions.py --device "cpu or gpu" --distance_map /path/to/distancemaps --seq /path/to/1D_sequence --label /path/to/labels

Jun 17, 2017 · As part of a project me and some teammates did a script that outputs visual maps of distances between residues. It uses Biopython. The module contact_map.py does what you are looking for. As an example, if you want to find the residues whose CA are below 5 you can run the following command: python3 contact_map.py pdb1cd8.ent -a CA -CA 5

We can obtain protein structure similarity based on distance maps by employing image comparison or distance map comparison methods. In this section, we have chosen the structure similarity index measure(SSIM) [ 52 ] to obtain protein structure similarity.