SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches | Zendy

G. V. HarshaRani | Zendy; Sahil Moza | Zendy; Naren Ramakrishnan | Zendy; Upinder S. Bhalla | Zendy

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SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches

Author(s) -

G. V. HarshaRani,

Sahil Moza,

Naren Ramakrishnan,

Upinder S. Bhalla

Publication year - 2021

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btab006

Subject(s) - bistability , network topology , computer science , interface (matter) , biological network , chemical space , distributed computing , topology (electrical circuits) , computer network , bioinformatics , materials science , parallel computing , drug discovery , biology , mathematics , optoelectronics , bubble , combinatorics , maximum bubble pressure method

Bistable biochemical switches are key motifs in cellular state decisions and long-term storage of cellular 'memory'. There are a few known biological switches that have been well characterized, however, these examples are insufficient for systematic surveys of properties of these important systems. Here we present a resource of all possible bistable biochemical reaction networks with up to six reactions between three molecules, and three reactions between four molecules. Over 35 000 reaction topologies were constructed by identifying unique combinations of reactions between a fixed number of molecules. Then, these topologies were populated with rates within a biologically realistic range. The Searchable Web Interface for Topologies of CHEmical Switches (SWITCHES, https://switches.ncbs.res.in) provides a bistability and parameter analysis of over seven million models from this systematic survey of chemical reaction space. This database will be useful for theoreticians interested in analyzing stability in chemical systems and also experimentalists for creating robust synthetic biological switches.

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