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توضیحات

Fast multiple protein structure alignment

ویژگی	مقدار
سیستم عامل	-
نام فایل	caretta-0.1.2
نام	caretta
نسخه کتابخانه	0.1.2
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Janani Durairaj, Mehmet Akdel
ایمیل نویسنده	janani.durairaj@gmail.com
آدرس صفحه اصلی	https://github.com/TurtleTools/caretta
آدرس اینترنتی	https://pypi.org/project/caretta/
مجوز	MIT License

<p align="center"><img src="https://raw.githubusercontent.com/TurtleTools/caretta/master/caretta_logo.png" width="300" title="Caretta Logo"></p> [![PyPI version](https://badge.fury.io/py/caretta.svg)](https://badge.fury.io/py/caretta) [![DOI](https://zenodo.org/badge/doi/10.1016/j.csbj.2020.03.011.svg)](http://dx.doi.org/10.1016/j.csbj.2020.03.011) [![DOI](https://zenodo.org/badge/doi/10.1101/2021.04.07.438777.svg)](http://dx.doi.org/10.1101/2021.04.07.438777) # Caretta-shape – A multiple protein structure alignment and feature extraction suite Caretta is a software-suite to perform multiple protein structure alignment and structure feature extraction. Visit the [demo server](http://bioinformatics.nl/caretta) to see caretta's capabilities. The server only allows alignment of up to 50 proteins at once. (This is currently down, will be back up soon!) The command-line tool and self-hosted web application do not have this restriction. The older, slower version of Caretta as described in https://doi.org/10.1016/j.csbj.2020.03.011 can be found at https://git.wur.nl/durai001/caretta ## Installation ### Requirements #### Operating system support 1. Linux and Mac * All capabilities are supported 2. Windows * The external tool **msms** is not available in Windows. Due to this: * Feature extraction is not available. * `features` argument in caretta-cli must always be run with `--only-dssp`. * `caretta-app` is not available. #### Software Caretta works with Python 3.7+ Run the following commands to install required external dependencies (Mac and Linux only): ```bash conda install -c salilab dssp conda install -c bioconda msms ``` ### Install both the command-line interface and the web-application (Mac and Linux only): ```bash pip install "caretta[GUI] @ git+https://github.com/TurtleTools/caretta.git" ``` ### Install only the command-line interface: ```bash pip install git+https://github.com/TurtleTools/caretta.git ``` ### Environment variables: ```bash export OMP_NUM_THREADS=1 # this should always be 1 export NUMBA_NUM_THREADS=20 # change to required number of threads ``` ## Usage ### Command-line Usage ```bash caretta-cli input_pdb_folder # e.g. caretta-cli test_data ``` Options: ``` Usage: caretta-cli [OPTIONS] INPUT_PDB Align protein structures using Caretta. Writes the resulting sequence alignment and superposed PDB files to "caretta_results". Optionally also outputs a set of aligned feature matrices, or the python class with intermediate structures made during progressive alignment. Arguments: INPUT_PDB A folder with input protein files [required] Options: -p FLOAT gap open penalty [default: 1.0] -e FLOAT gap extend penalty [default: 0.01] -c, --consensus-weight FLOAT weight well-aligned segments to reduce gaps in these areas [default: 1.0] -f, --full Use all vs. all pairwise alignment for distance matrix calculation (much slower) [default: False] -o, --output PATH folder to store output files [default: caretta_results] --fasta / --no-fasta write alignment in FASTA file format [default: True] --pdb / --no-pdb write PDB files superposed according to alignment [default: True] -t, --threads INTEGER number of threads to use for feature extraction [default: 4] --features extract and write aligned features as a dictionary of NumPy arrays into a pickle file [default: False] --only-dssp extract only DSSP features [default: False] --class write StructureMultiple class with intermediate structures and tree to pickle file [default: False] --matrix write distance matrix to file [default: False] -v, --verbose Control verbosity [default: True] --install-completion [bash|zsh|fish|powershell|pwsh] Install completion for the specified shell. --show-completion [bash|zsh|fish|powershell|pwsh] Show completion for the specified shell, to copy it or customize the installation. --help Show this message and exit. ``` ### Web-application Usage (Mac and Linux only) ```bash caretta-app <host-ip> <port> # e.g. caretta-app localhost 8091 ``` Then go to localhost:8091/caretta in a browser window. ### Features * `dssp_NH_O_1_index`, `dssp_NH_O_1_energy`, `dssp_NH_O_2_index`, `dssp_NH_O_2_energy`, `dssp_O_NH_1_index`, `dssp_O_NH_1_energy`, `dssp_O_NH_2_index`, `dssp_O_NH_2_energy`: hydrogen bonds; e.g. -3,-1.4 means: if this residue is residue i then N-H of I is h-bonded to C=O of I-3 with an electrostatic H-bond energy of -1.4 kcal/mol. There are two columns for each type of H-bond, to allow for bifurcated H-bonds. * `dssp_acc`: number of water molecules in contact with this residue *10. or residue water exposed surface in Angstrom^2. * `dssp_alpha`: virtual torsion angle (dihedral angle) defined by the four Cα atoms of residues I-1,I,I+1,I+2. Used to define chirality. * `dssp_kappa`: virtual bond angle (bend angle) defined by the three Cα atoms of residues I-2,I,I+2. Used to define bend (structure code ‘S’). * `dssp_phi`: IUPAC peptide backbone torsion angles. * `dssp_psi`: IUPAC peptide backbone torsion angles. * `dssp_tco`: cosine of angle between C=O of residue I and C=O of residue I-1. For α-helices, TCO is near +1, for β-sheets TCO is near -1. * `anm_ca`: Fluctuations of alpha carbon atoms based on an Anisotropic network model * `anm_cb`: Fluctuations of beta carbon atoms based on an Anisotropic network model * `gnm_ca`: Fluctuations of alpha carbon atoms based on a Gaussian network model * `gnm_cb`: Fluctuations of beta carbon atoms based on a Gaussian network model * `depth_ca`: Depths of alpha carbon atoms * `depth_cb`: Depths of beta carbon atoms * `depth_mean`: Mean depth of residues ## Publications Janani Durairaj, Mehmet Akdel, Dick de Ridder, Aalt DJ can Dijk. "Fast and adaptive protein structure representations for machine learning." [Machine Learning for Structural Biology Workshop](mlsb.io), NeurIPS 2020 (https://doi.org/10.1101/2021.04.07.438777) Poster: ![MLSB2020.png](https://raw.githubusercontent.com/TurtleTools/caretta/master/MLSB2020.png) Akdel, Mehmet, Janani Durairaj, Dick de Ridder, and Aalt DJ van Dijk. "Caretta-A Multiple Protein Structure Alignment and Feature Extraction Suite." Computational and Structural Biotechnology Journal (2020). (https://doi.org/10.1016/j.csbj.2020.03.011)

نیازمندی

مقدار	نام
-	numpy
-	numba
-	scipy
-	prody
-	biopython
-	typer
-	pyparsing
-	geometricus
-	arviz
==1.3.1	dash
==0.1.4	dash-bio
-	cryptography
==1.2.1	dash-core-components
==1.0.1	dash-html-components
==1.1.0	dash-renderer
==3.7.1	plotly
-	flask

زبان مورد نیاز

مقدار	نام
>=3.7	Python

نحوه نصب

نصب پکیج whl caretta-0.1.2:

pip install caretta-0.1.2.whl

نصب پکیج tar.gz caretta-0.1.2:

pip install caretta-0.1.2.tar.gz