BNICE specifications


Unique identifier OMICS_20283
Alternative name Biochemical Network Integrated Computational Explorer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No


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Publications for Biochemical Network Integrated Computational Explorer

BNICE in publications

PMCID: 5766603
PMID: 29330441
DOI: 10.1038/s41467-017-02362-x

[…] changes, or molecule fingerprint changes between substrates and products have been encoded as reaction rule operators in formats such as bem, rdm, and smirks. pathway prediction techniques such as bnice, xtms, um-pps, pathpred, route designer, and gem-path employ reaction rule operators for a single molecular target iteratively in a retrosynthetic fashion so as to identify a bioconversion […]

PMCID: 5736515
PMID: 29260340
DOI: 10.1186/s13321-017-0252-9

[…] coli. more precisely, we used as a source set all the metabolites present in e. coli ijo1366 model []. we first tested the two rule sets aforementioned, a set of about 100 reaction rules part of the bnice framework [] and a set of 50 reaction rules developed with the sympheny software []. the reaction rules coded in the form of smarts string are provided in supplementary at, […]

PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] of hypothetical reactions can be developed using (but not limited to) five different reaction operators which encode chemical transformation mechanisms in a different manner as described here: (i) bnice uses bond-electron matrix (bem) to define non-bonded valence electrons and bond orders ; (ii) xtms uses a molecular signature to generate reaction rules based on substructure of adjacent atoms […]

PMCID: 5662904
PMID: 29123506
DOI: 10.3389/fmicb.2017.02060

[…] constraint-based modeling can account for heterologous expression if the gene and function are known. there are fewer options available to computational approach to develop de novo pathways. bnice was able to identify novel pathways using a “generalized enzyme reaction” according to the third level classification. each pathway was examined on a basis of thermodynamics for chemical […]

PMCID: 5602787
PMID: 29086092
DOI: 10.1186/s13321-017-0239-6

[…] extend beyond the data stored in curated metabolic databases. other databases like atlas [] and xtms [] store information on extended search spaces and even apply existing pathfinding techniques (bnice [, ] and retropath [], respectively) to these spaces. metabolic pathfinding may not be the main focus of retrosynthesis algorithms and expanded databases; however, these resources […]

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BNICE institution(s)
Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, USA
BNICE funding source(s)
Supported by the United States Department of Energy, Genomes to Life Program.

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