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BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains
2004
Bioinformatics
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, potential post-translational modifications and interactions of the domains of signaling molecules. ...
BioNetGen allows a user to create a computational model that characterizes the dynamics of a signal transduction system, and that accounts comprehensively and precisely for specified enzymatic activities ...
NOTE ADDED IN PROOF BioNetGen can now handle complexes of more than two multistate species. See the BioNetGen web site for details. ...
doi:10.1093/bioinformatics/bth378
pmid:15217809
fatcat:3jc7bm47dzchhfos57cbu7h24a
DNA as a Universal Substrate for Chemical Kinetics
[chapter]
2009
Lecture Notes in Computer Science
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A preliminary version of this work appeared as ref. 52. ...
in full generality. ...
the corresponding systems of coupled chemical reactions (1) (2) (3) (4) . ...
doi:10.1007/978-3-642-03076-5_6
fatcat:7svfsav4xrhc7hcuc2oblp5s2a
DNA as a universal substrate for chemical kinetics
2010
Proceedings of the National Academy of Sciences of the United States of America
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A preliminary version of this work appeared as ref. 52. ...
in full generality. ...
the corresponding systems of coupled chemical reactions (1) (2) (3) (4) . ...
doi:10.1073/pnas.0909380107
pmid:20203007
pmcid:PMC2851759
fatcat:hap522zhdfdgpnyld4qdvwvbre
Graphical rule-based representation of signal-transduction networks
2005
Proceedings of the 2005 ACM symposium on Applied computing - SAC '05
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representations, such as a long list of chemical species and reactions in a network, tend to be incomprehensible. ...
As a result, interactions of signaling proteins have the potential to generate a combinatorially large number of complexes and modified states, and representing signal-transduction networks can be challenging ...
ACKNOWLEDGEMENTS This work was supported by grants GM35556 and RR18754 from the National Institutes of Health and by the Department of Energy through contract W-7405-ENG-36. ...
doi:10.1145/1066677.1066712
dblp:conf/sac/FaederBH05
fatcat:f65bigudgfgqlhp4u7qwnfx6ei
Rule-Based Generation of Thermochemical Routes to Biomass Conversion
2010
Industrial & Engineering Chemistry Research
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This tool can be used in exploring reaction pathways in biomass conversion as well as in modeling the reaction systems involved in the different stages of biofuels production. ...
Cheminformatics and graph-theoretic techniques have been used to develop a reaction generator capable of handling homogeneous and heterogeneous reactions in the thermochemical routes to biomass conversion ...
In this paper, a rule-based programming tool is presented that can generate such a complex reaction system and provide the user with the ability to handle the various types of chemistry typical in biomass ...
doi:10.1021/ie100546t
fatcat:cykhymnz4jgtjmf4inmgfeapsq
The complexity of complexes in signal transduction
2003
Biotechnology and Bioengineering
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Here, we review the role of multicomponent complexes in signal transduction and advocate the use of mathematical models that incorporate detail at the level of molecular domains to study this important ...
Complex formation is governed by conditional interactions among multivalent signaling molecules and influenced by quantitative properties of both the components in a system and the system itself. ...
The number of parameters in the model is comparable to the number of molecular domains, not the number of chemical species or reactions. ...
doi:10.1002/bit.10842
pmid:14708119
fatcat:myj34vbl4nhspcsvigiyrmk6ii
Simplifying Chemical Reaction Network Implementations with Two-Stranded DNA Building Blocks
2020
International Meeting on DNA Computing
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In molecular programming, the Chemical Reaction Network model is often used to describe real or hypothetical systems. ...
This also suggests that it would be useful to optimize the result of such a compilation, and in general to find effective ways to design better DNA strand displacement systems. ...
The Chemical Reaction Network (CRN) model is often used to describe systems of interacting molecules. ...
doi:10.4230/lipics.dna.2020.2
dblp:conf/dna/JohnsonQ20
fatcat:bjfq5x7gxrbkjoek6ineiiwice
Enzyme-free nucleic acid dynamical systems
2017
Science
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Oscillations were observed in directly measured rates of the three implemented reaction modules and in the extrapolated concentrations of oligonucleotides representing formal species. ...
(Inset) A part of the strand displacement implementation: An input strand initiates a cascade that displaces two output strands from a complex, in the process converting two "fuel molecules" (present in ...
We obtained the domain-level specification of the fuels for driving the autocatalytic reaction by starting with the general prescription shown Fig. 1E and by replacing the domains of U, V, X, and Y by ...
doi:10.1126/science.aal2052
pmid:29242317
fatcat:xnpgpinvvvf7fh5liqylcqhdvu
A sound approach to self-assembly
2020
Nature Chemistry
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Now, liquid vibrations induced by audible sound have been shown to direct the formation of spatiotemporal patterns in switchable chemical systems and assemblies. ...
Controlling the formation of ordered and predictable patterns in dissipative reaction-diffusion processes is challenging. ...
Pappas ✉ Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands. ✉ e-mail: c.pappas@rug.nl Published online: 24 August 2020 https://doi.org/10.1038/s41557 ...
doi:10.1038/s41557-020-0526-0
pmid:32839600
fatcat:hrypqs2qejelbddaopwtmmgbq4
RuleDSD: A Rule-based Modelling and Simulation Tool for DNA Strand Displacement Systems
2020
Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies
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The input to RuleDSD is a domain-level model of a DSD system, where each initial DNA complex is described at the level of named pairing domains. ...
rules of DNA strand displacement reactions to the ensemble of initial species. ...
Figure 6 : The RuleDSD-generated chemical reaction network of our representative example of a catalytic DSD system. ...
doi:10.5220/0008979101580167
dblp:conf/biostec/GautamLO20
fatcat:cjif4bxwyng2vkagscofy2bzn4
Self-Organized Stationary Patterns in Networks of Bistable Chemical Reactions
2016
Angewandte Chemie
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In biological context, many chemical reactions take place in discrete units, e.g., in cells, that form a complex network. [1, 2] Similarly, recent advances in microfabrication allow the generation of engineered ...
The method was also demonstrated to localization of chemical reactions to network substructures and identification of critical sites whose activation results in complete activation of the system. ...
K. acknowledge financial support by the LASAGNE (Contract No.318132) EU project. M. S. and I. Z. K. acknowledge support from National Science Foundation CHE-1465013. ...
doi:10.1002/ange.201607030
fatcat:2vrkfn55rjc4xenwefo2vqij4a
Towards a Planning-Based Approach to the Automated Design of Chemical Processes
2013
International Conference of the Italian Association for Artificial Intelligence
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The manual specification of such processes can be time-consuming and error-prone, due to the high number of reactions involved and their complex chemical conditions. ...
The design of chemical processes is a central problem in organic chemistry. ...
The work of Andrea Marrella has been partly supported by the SAPIENZA grants SUPER and "Premio Ricercatori Under-40". ...
dblp:conf/aiia/MasoumiMS13
fatcat:jmh5lu6fsfgrxb5mbvpa66fuae
Protein Chemical Ligation as an Invaluable Tool for Structural NMR
2005
Protein Peptide Letters
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Due to the exquisite sensitivity of the NMR chemical shift to the changes in the chemical environment, it was concluded that there is no direct interaction between domains 1.1 and 4.2. ...
Method The general methodology of expressed protein ligation is based on the reaction between the C-terminal thioester of the N-terminal segment of the protein and the Nterminal cysteine residue of the ...
doi:10.2174/0929866054864229
pmid:16305546
fatcat:drcernf7ezcppexx2447y3t7ji
Enzyme-Free Nucleic Acid Dynamical Systems
[article]
2017
biorxiv/medrxiv
pre-print
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Abstract coupled chemical reactions have been proposed as a programming language for complex dynamics, along with their systematic implementation using short synthetic DNA molecules. ...
Can simpler molecular mechanisms, designed from scratch, exhibit the same range of behaviors? ...
The success of an experimental realization is determined by how well the system behaves in accordance with the domain-level model. ...
doi:10.1101/138420
fatcat:6c56kjr6frafrdt3leawfjewta
Self-Organized Stationary Patterns in Networks of Bistable Chemical Reactions
2016
Angewandte Chemie International Edition
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The method also enabled the localization of chemical reactions to network substructures and the identification of critical sites whose activation results in complete activation of the system. ...
The results show that the pattern formation can be described by the identification of domains that can be activated individually or in combinations. ...
K. acknowledge financial support by the LASAGNE (Contract No.318132) EU project. M. S. and I. Z. K. acknowledge support from National Science Foundation CHE-1465013. ...
doi:10.1002/anie.201607030
pmid:27654486
fatcat:ztgljdhqlrd2bks366gqvjqoda
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