SPMweb

Shortest Path Map Web Tool

SPMweb is the online webserver of the Shortest Path Map (SPM) tool for identifying the key conformationally- relevant positions of a given enzyme structure and dynamics.

The server is built on top of the DynaComm.py code and enables the calculation and visualization of the SPM pathways. SPM applications expand from computational enzyme design, especially if combined with other tools to identify the preferred substitution at the identified position, but also to rationalizing allosteric regulation, and even cryptic pocket identification for drug discovery. The simple user interface and setup make the SPM tool accessible to the whole scientific community.

This tool was developed thanks to the funding from the European Research Council – Starting Grant project ERC-2015-StG-679001.

How to use →

SPMweb is easy-to-use as it only requires three input files: the three-dimensional structure of the protein of interest, and the two matrices (distance and correlation) previously computed from a Molecular Dynamics simulation. Click for more information.

Get access →

To use SPMweb, an email should be sent to: spmosuna@udg.edu to receive a token to run the webserver. This is free for academic users. For commercial users, an email should be sent to the same email account.

More information →

Learn more about Shortest Path Map tool in the following publication: Osuna S. The challenge of predicting distal active site mutations in computational enzyme design. WIREs Comput Mol Sci. 2021; 11:e1502.

How to cite →

  • G. Casadevall, J. Casadevall, C. Duran, S. Osuna, The Shortest Path Method (SPM) webserver for computational enzyme design, Protein Eng. Des. Sel. 2024; 37:gzae005
  • Osuna S. The challenge of predicting distal active site mutations in computational enzyme design. WIREs Comput Mol Sci. 2021; 11:e1502.

Submit your Job

Or drag and drop file here with extension npy or dat

Or drag and drop file here with extension npy or dat

Or drag and drop file here with extension pdb

SPM SIGNIFICANCE THRESHOLD

0.10.8
Current: 0.3 - 1.0

DISTANCE THRESHOLD

510
Current: 6

How to use

SPMweb is easy-to-use as it only requires three input files: the three-dimensional structure of the protein of interest, and the two matrices (distance and correlation) previously computed from a Molecular Dynamics simulation.

The total size of uploaded files must not exceed 4MB.

For information on how to generate the files for SPM construction, check this publication: G. Casadevall, J. Casadevall, C. Duran, S. Osuna, The Shortest Path Method (SPM) webserver for computational enzyme design, Protein Eng. Des. Sel. 2024; 37:gzae005

Terms of Service

  1. Acceptance of Terms
    By using SPMweb, you agree to the following Terms of Use. If you do not agree to these terms and conditions, you are not authorized to use this website.
  2. Description of Service
    SPMweb provides a tool for processing scientific non-commercial data. Users can upload up to three data files, which the website processes to produce a scientific output file for non-commercial purposes
  3. User Conduct
    • You agree to use the website only for lawful purposes.
    • You are responsible for any data you upload.
    • You must not upload any data that infringes on intellectual property rights or contains sensitive personal information.
    • You must cite the following academic publications (10.1002/wcms.1502,10.1093/protein/gzae005), if you use any information derived from this webserver.

License: CC-BY-NC-ND

G. Casadevall, J. Casadevall, C. Duran, S. Osuna © Universitat de Girona, Girona, 2024, All rights reserved.