Metadata-Version: 2.1
Name: pybmrb
Version: 1.2.96
Summary: PyBMRB provides tools to visualize chemical shift data in BMRB
Home-page: https://github.com/uwbmrb/PyBMRB
Author: Kumaran Baskaran
Author-email: baskaran@uchc.edu
License: MIT
Description: # PyBMRB
        [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/uwbmrb/PyBMRB/master?filepath=pybmrb%2Fexamples) Click the launcher to try PyBMRB on a live Jupyter Notebook.
        ## Biological Magnetic Resonance data Bank (BMRB)
        [BMRB](http://www.bmrb.wisc.edu/) collects, annotates, archives, and disseminates (worldwide in the public domain)
         the important spectral and quantitative data derived from NMR spectroscopic 
         investigations of biological macromolecules and metabolites. The goal is to empower 
         scientists in their analysis of the structure, dynamics, and chemistry of biological 
         systems and to support further development of the field of 
         biomolecular NMR spectroscopy. 
         
         BMRB maintains its data in a relational data base and also as flat files in [NMR-STAR](https://doi.org/10.1007/s10858-018-0220-3)
          format. It also provides data access via API and provide software tools to handle NMR-STAR files. 
         [PyNMRSTAR](https://github.com/uwbmrb/PyNMRSTAR) is one such tool to facilitate read, write and parse
         NMR-STAR files. [PyBMRB](https://github.com/uwbmrb/PyBMRB) enhances the usability of BMRB data 
         and data access and visualization of chemical shift data from BMRB. 
         
         ## Data visualization
         
        PyBMRB uses modern python visualization tool [plotly](https://plot.ly/python/) for 
        its visualization. It features chemical shift histograms of 
        standard amino acids from BMRB data base and N<sup>15</sup>-HSQC peak position simulation
        for any given BMRB entry (or) list of BMRB entries (or) from a local assigned chemical 
        shift list in NMR-STAR format. Random coil N<sup>15</sup>-HSQC simulation based on BMRB 
        database statistics is also included.  
        
        This library can produce stand alone interactive visualizations as an html file or it can 
        be used in a [Jupyter Notebook](https://jupyter.org/). Example notebooks can be found 
        [here](https://github.com/uwbmrb/PyBMRB/tree/master/pybmrb/examples)
        
        ### Installation
        PyBMRB is available in [Python Package Index (PIP)](https://pypi.org/project/pybmrb/). It can be easily 
        installed with the following command
        >pip install pybmrb
        
        To install from the source, clone or download the source and go to the folder which contains 'setup.py' 
        and run the following command
        >pip install .
        
        If necessary use 'sudo'. 
        ### Chemical shift Histogram
        BMRB serves Nuclear Magnetic Resonance(NMR) community by providing 
        high quality curated chemical shift data of various biologically important 
        macro molecules like proteins and nucleic acids and small molecules like ligands , co-factors,
        small peptides and metabolites. Chemical shift distribution of an atom in an amino acid or 
        nucleic acid helps us to understand its diverse chemical environment.
        Chemical shift histograms from a database like BMRB will help
        us to understand the biophysical nature bio-molecules and provides a priory 
        probabilities for resonance assignments.
        
        #### Conditional Histogram
        Chemical shift assignment in a multi-dimensional NMR experiment is 
        a biggest challenge. PyBMRB could help the process by generating 
        conditional histogram. If partial assignments of a particular 
        amnio acid is available, then PyBMRB could estimate the chemical shift
        distribution of an unassigned atom in that amino acid only from those entries
         whose chemical shifts are similar to the given list for that 
         particular amino acid. 
        
        
        #### Examples in Notebook
        Chemical shift histogram [examples notebook](https://github.com/uwbmrb/PyBMRB/tree/master/pybmrb/examples/histogram.ipynb) 
        can be found [here](https://github.com/uwbmrb/PyBMRB/tree/master/pybmrb/examples/histogram.ipynb). 
        The output might look like [this](https://htmlpreview.github.io/?https://github.com/uwbmrb/PyBMRB/blob/master/pybmrb/examples/histogram.html)  
        
        ### N<sup>15</sup>-HSQC Simulation.
        
        N<sup>15</sup>-HSQC is one of the most common and useful NMR experiment.
        It carries signatures of folded state, ligand interaction and experimental environments 
        like pH and temperature. BMRB contains thousands of assigned chemical shifts
        of various bio-molecules. PyBMRB make use of this data to simulate N<sup>15</sup>-HSQC 
        peak positions for any BMRB entry. Its also possible to compare N<sup>15</sup>-HSQC 
        spectra of different entries or BMRB entries with user generated
         chemical shift information in NMR-STAR format. 
         
         #### N<sup>15</sup>-HSQC spectrum from sequence. 
         As an experiment, BMRB developed tools to simulate random coil
         N<sup>15</sup>-HSQC spectrum for a given protein sequence using 
         database statistics. Assuming the fact that in BMRB, small segments 
         of given sequence might exists in all possible confirmations, 
         one could calculate the chemical shift of an atom in random 
         confirmation by averaging the chemical shifts of small segments
         over the entire database
         
         #### Examples in Notebook
         N<sup>15</sup>-HSQC [examples notebook](https://github.com/uwbmrb/PyBMRB/tree/master/pybmrb/examples/n15hsqc.ipynb) 
         can be found [here](https://github.com/uwbmrb/PyBMRB/tree/master/pybmrb/examples/n15hsqc.ipynb)
         The output of the notebook looks like [this](https://htmlpreview.github.io/?https://github.com/uwbmrb/PyBMRB/blob/master/pybmrb/examples/n15hsqc.html)
         
        
Keywords: bmrb,hsqc,chemical shift,nmrstar,biomagresbank,biological magnetic resonance bank
Platform: UNKNOWN
Description-Content-Type: text/markdown
