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BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

M. L. Blinov, J. R. Faeder, B. Goldstein, W. S. Hlavacek
2004 Bioinformatics  
, 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]

David Soloveichik, Georg Seelig, Erik Winfree
2009 Lecture Notes in Computer Science  
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

D. Soloveichik, G. Seelig, E. Winfree
2010 Proceedings of the National Academy of Sciences of the United States of America  
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

James R. Faeder, Michael L. Blinov, William S. Hlavacek
2005 Proceedings of the 2005 ACM symposium on Applied computing - SAC '05  
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

Srinivas Rangarajan, Aditya Bhan, Prodromos Daoutidis
2010 Industrial & Engineering Chemistry Research  
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

William S. Hlavacek, James R. Faeder, Michael L. Blinov, Alan S. Perelson, Byron Goldstein
2003 Biotechnology and Bioengineering  
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

Robert F. Johnson, Lulu Qian, Matthew J. Patitz, Cody Geary
2020 International Meeting on DNA Computing  
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

Niranjan Srinivas, James Parkin, Georg Seelig, Erik Winfree, David Soloveichik
2017 Science  
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

Charalampos G. Pappas
2020 Nature Chemistry  
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

Vinay Gautam, Shiting Long, Pekka Orponen
2020 Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies  
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

Nikos E. Kouvaris, Michael Sebek, Alexander S. Mikhailov, István Z. Kiss
2016 Angewandte Chemie  
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

Arman Masoumi, Andrea Marrella, Mikhail Soutchanski
2013 International Conference of the Italian Association for Artificial Intelligence  
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

Alexander Shekhtman
2005 Protein Peptide Letters  
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]

Niranjan Srinivas, James Parkin, Georg Seelig, Erik Winfree, David Soloveichik
2017 biorxiv/medrxiv   pre-print
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

Nikos E. Kouvaris, Michael Sebek, Alexander S. Mikhailov, István Z. Kiss
2016 Angewandte Chemie International Edition  
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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