Mollack: a web server for the automated creation of conformational ensembles for intrinsically disordered proteins

Zachary Ziegler; Molly Schmidt; Thomas Gurry; Virginia Burger; Collin M Stultz

doi:10.1093/bioinformatics/btw200

Mollack: a web server for the automated creation of conformational ensembles for intrinsically disordered proteins

Bioinformatics. 2016 Aug 15;32(16):2545-7. doi: 10.1093/bioinformatics/btw200. Epub 2016 Apr 19.

Authors

Zachary Ziegler¹, Molly Schmidt², Thomas Gurry³, Virginia Burger⁴, Collin M Stultz⁵

Affiliations

¹ Cornell University, Ithaca, NY 14850, USA Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA.
² Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA.
³ Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA.
⁴ Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA.
⁵ Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA The Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA.

PMID: 27153636
DOI: 10.1093/bioinformatics/btw200

Abstract

Intrinsically disordered proteins (IDPs) play central roles in many biological processes. Consequently, an accurate description of the disordered state is an important step towards a comprehensive understanding of a number of important biological functions. In this work we describe a new web server, Mollack, for the automated construction of unfolded ensembles that uses both experimental and molecular simulation data to construct models for the unfolded state. An important aspect of the method is that it calculates a quantitative estimate of the uncertainty in the constructed ensemble, thereby providing an objective measure of the quality of the final model. Overall, Mollack facilitates structure-function studies of disordered proteins.

Availability and implementation: http://cmstultz-mollack.mit.edu

Contact: cmstultz@mit.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Computers*
Internet
Intrinsically Disordered Proteins*
Protein Conformation

Substances

Intrinsically Disordered Proteins