ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design

Wood, C. W., Heal, J. W., Thomson, A. R. , Bartlett, G. J., Ibarra, A. A., Brady, R. L., Sessions, R. B. and Woolfson, D. N. (2017) ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design. Bioinformatics, 33(19), pp. 3043-3050. (doi: 10.1093/bioinformatics/btx352) (PMID:28582565) (PMCID:PMC5870769)

Abstract

Motivation: The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users. Results: Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico. ISAMBARD addresses a standing issue in protein design, namely, how to introduce backbone variability in a controlled manner. This is achieved through the generalization of tools for parametric modelling, describing the overall shape of proteins geometrically, and without input from experimentally determined structures. This will allow backbone conformations for entire folds and assemblies not observed in nature to be generated de novo, that is, to access the ‘dark matter of protein-fold space’. We anticipate that ISAMBARD will find broad applications in biomolecular design, biotechnology and synthetic biology. Availability and implementation: A current stable build can be downloaded from the python package index (https://pypi.python.org/pypi/isambard/) with development builds available on GitHub (https://github.com/woolfson-group/) along with documentation, tutorial material and all the scripts used to generate the data described in this paper. Contact:[e-mail] or [e-mail] Supplementary information:Supplementary data are available at Bioinformatics online.

• Item Type: Articles
• Additional Information: CWW is supported by the Biotechnology and Biological Sciences Research Council South West Doctoral Training Partnership. This work was supported by grants from the Biotechnology and Biological Sciences Research Council (BB/J008990/1) and the European Research Council (340764) to DNW. DNW holds a Royal Society Wolfson Research Merit Award.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Thomson, Dr Drew
• Authors: Wood, C. W., Heal, J. W., Thomson, A. R., Bartlett, G. J., Ibarra, A. A., Brady, R. L., Sessions, R. B., and Woolfson, D. N.
• College/School: College of Science and Engineering > School of Chemistry
• Journal Name: Bioinformatics
• Publisher: Oxford University Press
• ISSN: 1367-4803
• ISSN (Online): 1460-2059
• Published Online: 05 June 2017
• Copyright Holders: Copyright © 2017 The Authors
• First Published: First published in Bioinformatics 33(19): 3043-3050
• Publisher Policy: Reproduced under a Creative Commons license