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Number of citations per year for the bioinformatics software tool BNICE

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This map represents all the scientific publications referring to BNICE per scientific context
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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 citations


Pathway design using de novo steps through uncharted biochemical spaces

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

[…] ty 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 from […]


Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

J Cheminform
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, alon […]


Production of C2–C4 diols from renewable bioresources: new metabolic pathways and metabolic engineering strategies

Biotechnol Biofuels
PMCID: 5727944
PMID: 29255482
DOI: 10.1186/s13068-017-0992-9

[…] d bioinformatics, different algorithms and prediction tools have been developed to aid in in silico pathway design and metabolic engineering [–]. Especially, several pathway prediction tools, such as BNICE and RetroPath which consider also promiscuous enzyme reactions, can be used for prediction and prioritization of various possible pathways to a given compound [, ]. In these computational framew […]


A review of computational tools for design and reconstruction of metabolic pathways

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

[…] a known reaction to a rule due to the inherent assumptions in their method to encode chemical transformation mechanisms . In particular, stereochemical changes are often overlooked, including BEM (in BNICE) and molecular signatures (in XTMS), as they do not contain chiral center information . As a result, the predicted pathway would use stereoisomers (such as l-alanine and d-alanine) interchangeab […]


Challenges and Advances for Genetic Engineering of Non model Bacteria and Uses in Consolidated Bioprocessing

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

[…] rganisms.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 formati […]


A review of parameters and heuristics for guiding metabolic pathfinding

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

[…] ctions from metabolic databases and (2) help expand an existing metabolic network created based on a metabolic database.Reaction rules are based heavily on structural representations of compounds. In BNICE [, ], compounds are represented as an atom-bond matrix, and the reactions are represented as the difference between the matrices of the substrate and product compounds (Fig. b). With this more g […]

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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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