DOI: 10.5281/zenodo.8382584
title: rbLEC - restricted backbone Local Euler Characteristic - from CATH database

description: ----------------------------------------------------------------------------------------------------------------------------------- <strong>Author: Rodrigo A. Moreira (C) 2023<br> https://orcid.org/0000-0002-7605-8722<br> LICENSE: CC BY-NC-ND 4.0 (https://creativecommons.org/licenses/by-nc-nd/4.0/)</strong> ---------------------------------------------------------------------------------------------------------------------------------- <strong>rbLEC - Local Euler Charactersitics - from CATH database</strong> ---------------------------------------------------------------------------------------------------------------------------------- <strong>A. rbLEC NETWORK</strong> [I] The networks for each PDB[1] structure is defined by the PDB atoms N,CA,C of each residue as nodes of a graph G.<br> [II] An edge of G is set if the distance between two atom in [I] is greater than 2.0 Angstrons.<br> [III] The graph G is defined in the files with extensions ".network_backboneRE_heavy_gt2" Equation (1) [6,7]<br> \begin{equation}<br> \chi = \sum_{k=1}^{N} \kappa_k = \sum_{k=1}^{N} \underbrace{ \left(1 + \sum_{l=1}^{\infty} (-1)^{l} \frac{v_{l-1}}{l+1} \right)_{k}}_{\kappa_k}<br> \end{equation} Equation (2)<br> \begin{equation}<br> LEC = \sum_{m \in R} \kappa_m = \kappa_{N} + \kappa_{CA} + \kappa_{C}<br> \end{equation} <strong>B. FILENAME EXTENSIONS</strong> <strong> B.1</strong> Basic files ".fixed"<br> PDB file after use of pdbfixer[2] in structures from CATH database. ".dssp"<br> Output of DSSP[3] software ".stride"<br> Output of STRIDE[4] software <strong>B.2</strong> Data files ".network_backboneRE_heavy_gt2" - Generate by <strong>D.2</strong> below.<br> Describe the network graph, as described in <strong>A.</strong> above. ".knill_curvature" - Generate by <strong>D.1</strong> below.<br> Contain the filtration of kappas for each vertice of the network. ".residues_curvature" - Generate by <strong>D.1</strong> below.<br> They are the filtration of LEC, Equation (2) above, for each residue, namely summation of 3 kappas from respective '.knill_curvature', correspoings to PDB atoms N,CA and C, describe in <strong>A.</strong> above. ".label" - Generated by <strong>D.3 </strong>below<br> Extra file for easier assesment of structures. They have the same information about LEC as described in respective ".residue_curvature" file extensions, but merge also the information from ".dssp" and ".stride" classes as well as residue name and residue ID for each molecule.<br> Format of columns:<br> cutoff resname resid DSSP_class STRIDE_class LEC <strong>C. FOLDERS</strong> CATH_FIXED (after uncompress cath_fixed.tar.xz, approximately 13GB)<br> contains the fixed PDBs and LECs from CATH[5] database <strong>D. SOFTWARE</strong><br> <strong>D.1</strong> lec.py: compute the kappas in Equation (1) above.<br> Example usage:<br> $ python3 lec.py CATH_FIXED/2x0qA02/2x0qA02<br> It will create the files with extension ".kappas" and ".relec", which reproduces the respectively the files with extension "<strong>.knill_curvature</strong>" and "<strong>.residue_curvature</strong>". <strong> D.2</strong> pdb2network.lua: creates rbLEC network file (number of nodes and edges list) from PDB to be used as input by lec.py.<br> Example usage:<br> $ lua pdb2rbLEC.lua CATH_FIXED/2x0qA02/2x0qA02.fixed<br> Output reproduces the file CATH_FIXED/2x0qA02/2x0qA02.pdb.<strong>network_backboneRE_heavy_gt2</strong> <strong>D.3</strong> label.lua: create files with extension '*.label' from files '*.pdb.stride', '*.pdb.dssp' and '*.pdb.network_backboneRE_heavy_gt2.residues_curvature.<br> Example usage:<br> $ lua label.lua CATH_FIXED/2x0qA02/2x0qA02.pdb<br> Output reproduces the file CATH_FIXED/2x0qA02/2x0qA02.pdb.<strong>network_backboneRE_heavy_gt2.residues_curvature.label</strong> <strong>REFERENCES</strong><br> [1] Herman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H., Shindyalov, I., & Bourne, P. (2000). The protein data bank. Nucleic acids research, 28, 235–42.<br> [2] Eastman, P., Swails, J., Chodera, J., McGibbon, R., Zhao, Y., Beauchamp, K., Wang, L.P., Simmonett, A., Harrigan, M., Stern, C., & others (2017). OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS computational biology, 13(7), e1005659.<br> [3] Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers: Original Research on Biomolecules, 22(12), 2577–2637.<br> [4] Frishman, D., & Argos, P. (1995). Knowledge-based protein secondary structure assignment. Proteins: Structure, Function, and Bioinformatics, 23(4), 566–579.<br> [5] Knudsen, M., & Wiuf, C. (2010). The CATH database. Human genomics, 4(3), 1–6.<br> [6] Levitt, N. (1992). The Euler characteristic is the unique locally determined numerical homotopy invariant of finite complexes. Discrete & computational geometry, 7, 59–67.<br> [7] Knill, O. (2011). A graph theoretical Gauss-Bonnet-Chern theorem. arXiv preprint arXiv:1111.5395.
description: {"references": ["Herman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H., Shindyalov, I., & Bourne, P. (2000). The protein data bank. Nucleic acids research, 28, 235\u201342.", "Eastman, P., Swails, J., Chodera, J., McGibbon, R., Zhao, Y., Beauchamp, K., Wang, L.P., Simmonett, A., Harrigan, M., Stern, C., & others (2017). OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS computational biology, 13(7), e1005659.", "Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers: Original Research on Biomolecules, 22(12), 2577\u20132637.", "Frishman, D., & Argos, P. (1995). Knowledge-based protein secondary structure assignment. Proteins: Structure, Function, and Bioinformatics, 23(4), 566\u2013579.", "Knudsen, M., & Wiuf, C. (2010). The CATH database. Human genomics, 4(3), 1\u20136.", "Levitt, N. (1992). The Euler characteristic is the unique locally determined numerical homotopy invariant of finite complexes. Discrete & computational geometry, 7, 59\u201367.", "Knill, O. (2011). A graph theoretical Gauss-Bonnet-Chern theorem. arXiv preprint arXiv:1111.5395."]}