SPyCi-PDB

SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures. - Published in JOSS (2023)

https://github.com/julie-forman-kay-lab/spyci-pdb

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Structural Python (Back) Calculator Interface for PDBs

README.rst

SPyCi-PDB
=========
.. image:: https://github.com/julie-forman-kay-lab/SPyCi-PDB/blob/0e7b60d50a021d741dd7db4e2b9fbb9605fec95b/docs/spycipdb_ascii1.png

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.. image:: https://github.com/julie-forman-kay-lab/SPyCi-PDB/actions/workflows/ci.yml/badge.svg?branch=main
    :target: https://github.com/julie-forman-kay-lab/SPyCi-PDB/actions/workflows/ci.yml
    :alt: Test Status

.. image:: https://readthedocs.org/projects/spyci-pdb/badge/?version=stable
    :target: https://spyci-pdb.readthedocs.io/en/stable/?badge=stable
    :alt: Documentation Status

.. image:: https://joss.theoj.org/papers/10.21105/joss.04861/status.svg
   :target: https://doi.org/10.21105/joss.04861
   :alt: JOSS Paper

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   :alt: Zenodo Archive

**Structural Python (Back) Calculator Interface for PDBs**

**Goal:** User friendly Python3 based interface to generate back-calculated experimental data for singular and multiple (ensembles of) PDB structures.

**Back-Calculators:** The current back calculators integrated are:

#. NOE, J-Coupling, smFRET: Internal
#. Paramagnetic Relaxation Enhancement (PRE): distance-based and `DEERPREdict `_
#. Chemical shifts (CS): `UCBShift `_
#. SAXS: `CRYSOLv3 `_
#. Hydrodynamic Radius (Rh): `HullRadSAS `_
#. Residual Dipolar Couplings (RDC): `PALES `_

Please note for third-party software, installation instructions have been fully
documented and tested for the following Linux Ubuntu versions:
24.04 LTS, 22.04 LTS, 20.04 LTS, and 18.04 LTS.

To make new requests and/or additions, please see ``docs/contributing.rst``.

**Developer Notes:** project CI based on `@joaomcteixeira `_'s `Python-Project-Skeleton template `_.
Developed as a standalone program with integration into the IDPConformerGenerator platform in mind.

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Documentation
=============

More detailed documentation can be found at: https://spyci-pdb.readthedocs.io/en/stable/

Within the repository you can find:

#. Installation instructions in ``docs/installation.rst``.
#. Usage instructions in ``docs/usage.rst``.
#. See also the examples in the ``example/`` folder.

How to Cite
-----------

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If you use SPyCi-PDB, please cite::

    Liu et al., (2023). SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures.. Journal of Open Source Software, 8(85), 4861, https://doi.org/10.21105/joss.04861

.. end-citing

Version
=======

v0.6.0

Owner

JOSS Publication

SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures.

Published

May 10, 2023

DOI

10.21105/joss.04861

Volume 8, Issue 85, Page 4861

Authors

Zi Hao Liu
Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada

Oufan Zhang
Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of America

João M.c. Teixeira
Department of Biomedical Sciences, University of Padua, Padova, Italy

Jie Li
Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of America

Teresa Head-Gordon
Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of America, Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America, Department of Bioengineering, University of California, Berkeley, California, United States of America

Julie D. Forman-Kay
Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada

Editor

Antonia Mey

Tags

NMR SAXS smFRET Back-calculator PDB Structural Biology Proteins Biochemistry

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