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A Probabilistic Fragment-Based Protein Structure Prediction Algorithm

David Simoncini, Francois Berenger, Rojan Shrestha, Kam Y. J. Zhang, Yang Zhang
2012 PLoS ONE  
The best coarse-grained models produced by both methods were refined into allatom models and used in molecular replacement.  ...  In this work we present EdaFold, a new method for fragment-based protein structure prediction based on an Estimation of Distribution Algorithm.  ...  Taeho Jo and other members of our lab for stimulating discussions. We are grateful to Prof.  ... 
doi:10.1371/journal.pone.0038799 pmid:22829868 pmcid:PMC3400640 fatcat:rf5dugnhyngnratinlh2olrjku

Computing intrinsic noise of the genetic regulation modeled by Hill functions

Riccardo Ziraldo, Lan Ma
2018 Journal of Computational Systems Biology  
Heuristic SSA and LNA methods (hSSA and hLNA) have been applied to study stochastic models employing Hill functions.  ...  Specifically, SSA and LNA are applied to the full models that are expanded from the Hill functions containing only elementary reactions, while hSSA and hLNA are applied to reduced models where the Hill  ...  Hill functions.  ... 
doi:10.15744/2455-7625.3.101 fatcat:7cyhunrocrdkjo7brs7rju7j7i

Finding acceptable parameter regions of stochastic Hill functions for multisite phosphorylation mechanism

M. Chen, M. Ahmadian, L. T. Watson, Y. Cao
2020 Journal of Chemical Physics  
Different objective functions are investigated characterizing different features of the simulation-based empirical data, among which the approximate maximum log-likelihood method is recommended for general  ...  To reduce model complexity, this work aims at simplifying the multisite phosphorylation mechanism by a stochastic Hill function model.  ...  This paper, instead of validating the stochastic results against the deterministic results, will focus on optimizing the stochastic Hill function model for the multisite phosphorylation process, meaning  ... 
doi:10.1063/1.5143004 pmid:32241152 fatcat:ypc42pjxt5blfmck4nmcrg3sqe

Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d [article]

Dalibor Trapl, Vojtěch Spiwok
2020 arXiv   pre-print
These methods have a great potential in drug discovery because they can realistically model the structures of protein molecules targeted by drugs as well as the process of binding of a potential drug to  ...  its molecular target.  ...  for Biological data (ELIXIR CZ, LM2015047) for future sustainability.  ... 
arXiv:2009.02241v1 fatcat:3lbjt4py5ja6vkau3wxctulhlq

The Goodwin Model: Behind the Hill Function

Didier Gonze, Wassim Abou-Jaoudé, Nick Monk
2013 PLoS ONE  
The only source of non-linearity in this model is a Hill function, characterizing the repression process.  ...  We present here molecular models of the standard Goodwin model, based on single or multisite phosphorylation/dephosphorylation processes of a transcription factor, which have been previously shown to generate  ...  Acknowledgments The authors would like to thank Geneviève Dupont, Marcelle Kaufman, and Claude Gérard for helpful discussions and comments on the manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0069573 pmid:23936338 pmcid:PMC3731313 fatcat:tzy7tel2trgmlbkhcx2tykx44a

Quantitative and logic modelling of molecular and gene networks

Nicolas Le Novère
2015 Nature reviews genetics  
Quantitative and logic modelling are among the main methods currently used to model molecular and gene networks. Each approach comes with inherent advantages and weaknesses.  ...  Explanatory and predictive mathematical models are therefore useful for fully understanding and precisely engineering cellular functions.  ...  Thieffry for help with the bibliography.  ... 
doi:10.1038/nrg3885 pmid:25645874 pmcid:PMC4604653 fatcat:ewf5l5frsbfr3pu3ut5c4wcb6y

Hill functions for stochastic gene regulatory networks from master equations with split nodes and time-scale separation

Ovidiu Lipan, Cameron Ferwerda
2018 Physical review. E  
These stochastic Hill functions are presented in a closed analytical form so that they can be easily incorporated in models for large genetic regulatory networks.  ...  Here we present a method that allows for stochastic Hill functions to be constructed from the dynamical evolution of stochastic biocircuits with specific topologies.  ...  This method is easily scalable, allowing it to be used for either small or large genetic networks and, specifically for this study, generates stochastic Hill functions in a closed analytical form.  ... 
doi:10.1103/physreve.97.022413 pmid:29548212 fatcat:sefgzl4b5zfmtje6pfmsfrdaru

Mathematical Modeling of Biomolecular Network Dynamics [chapter]

Alexander V. Ratushny, Stephen A. Ramsey, John D. Aitchison
2011 Msphere  
Specifically, we describe a procedure for defining kinetic equations and parameters of biomolecular processes, and we illustrate the use of fractional activity functions for modeling gene expression regulation  ...  Define the list of processes and variables (molecular components: genes, RNAs, proteins, small molecules, intermediate complexes, etc.) that should be included in the model.  ...  Centers for Networks and  ... 
doi:10.1007/978-1-61779-276-2_21 pmid:21877294 pmcid:PMC4482237 fatcat:xfseidoyybhubki7wb6saafere

Regression Methods Based on Nearest Neighbors with Adaptive Distance Metrics Applied to a Polymerization Process

Silvia Curteanu, Florin Leon, Andra-Maria Mircea-Vicoveanu, Doina Logofătu
2021 Mathematics  
Empirical models based on sampled data can be useful for complex chemical engineering processes such as the free radical polymerization of methyl methacrylate achieved in a batch bulk process.  ...  An extensive comparative study is performed between three regression algorithms for this chemical process.  ...  Two reasons justify this choice: the complexity of the process, so the difficulties in modeling and also the fact that our group has tried different modeling methods for this system, so that the obtained  ... 
doi:10.3390/math9050547 doaj:63618c73e6e84f4587565c3b58d25020 fatcat:dp3w3plvw5b2hjo4nh5tmd5erm

Generalized binomial τ-leap method for biochemical kinetics incorporating both delay and intrinsic noise

André Leier, Tatiana T. Marquez-Lago, Kevin Burrage
2008 Journal of Chemical Physics  
We apply these ideas to two important genetic regulatory models, namely, the hes1 gene, implicated as a molecular clock, and a Her1/Her 7 model for coupled oscillating cells.  ...  These delayed processes can faithfully represent complex interactions and mechanisms that imply a number of spatiotemporal processes often not explicitly modeled such as transcription and translation,  ...  ACKNOWLEDGMENTS K.B. would like to thank the Australian Research Council for funding through the Federation Fellowship program.  ... 
doi:10.1063/1.2919124 pmid:18513050 fatcat:g7x4kp7zpzguxatuc7qyvgvhee

On the use of the Hill's model as local isotherm in the interpretation of the behaviour of the adsorption energy distributions

Yosra Ben Torkia, Mohamed Khalfaoui, A. Ben Lamine
2014 IOSR Journal of Applied Physics  
Activated carbons are reported to show promise for separation processes and natural gas storage, since they have a strongly heterogeneous surface.  ...  model as local isotherm.  ...  The adequate model which can express the general case is the Hill model, which is more powerful than Langmuir model.  ... 
doi:10.9790/4861-06316273 fatcat:7dui6ixsmza3zjggnan4y7zmvi

Search strategies for applied molecular evolution

Stuart A. Kauffman, William G. Macready
1995 Journal of Theoretical Biology  
Search of such libraries for useful molecules is an optimization problem on high-dimensional molecular fitness landscapes.  ...  We utilize a spin-glass-like model, the NK model, to analyze search strategies based on pooling, mutation, recombination and selective hill-climbing.  ...  Each was used over the remaining pool screening cycles, thereby generating eight terminal candidate pool optima for method 1 and 32 for method 2.  ... 
doi:10.1006/jtbi.1995.0074 pmid:7783452 fatcat:6n5w76dhenertizis5wawwrmjy

Biochemical clocks and molecular noise: Theoretical study of robustness factors

D. Gonze, J. Halloy, P. Gaspard
2002 Journal of Chemical Physics  
We report a study of the influence of molecular fluctuations on a limit-cycle model of circadian rhythms based on the regulatory network of a gene involved in a biochemical clock.  ...  The molecular fluctuations are described by a birth-and-death stochastic process ruled by the chemical master equation of Nicolis and co-workers and simulated by Gillespie's algorithm.  ...  Nicolis for support and encouragement in this research, as well as F. Baras  ... 
doi:10.1063/1.1475765 fatcat:qbnsxnxbvjejdilsjjjrtmogoi

Page 3485 of Mathematical Reviews Vol. , Issue 2004d [page]

2004 Mathematical Reviews  
Furthermore, this allows the use of any general solid modeling or visualization sys- tem as a molecular modeling interface.  ...  A critical step in this process is the computation and update of an exact boundary representation for the molecular surface (e.g., the Lee-Richards surface).  ... 

2SCP-05 Protein-ligand binding processes studied by coarse-grained molecular dynamics simulations(Prediction and analysis of protein functions from structural bioinformatics,Symposium,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))
2SCP-05 粗視化分子動力学シミュレーションで探るタンパク質・リガンド結合過程(構造バイオインフォマティクスによる蛋白質機能予測・解析,シンポジウム,第52回日本生物物理学会年会(2014年度))

Tohru Terada, Tatsuki Negami, Kentaro Shimizu
2014 Seibutsu Butsuri  
This pipeline contains the methods of knowledge-based modeling, domain/subunit docking, coarsegrained model refinement, and interface for structure mapping.  ...  We have explored the applicability of a coarsegrained molecular dynamics (CGMD) simulation to the study of proteinligand binding processes.  ...  This pipeline contains the methods of knowledge-based modeling, domain/subunit docking, coarsegrained model refinement, and interface for structure mapping.  ... 
doi:10.2142/biophys.54.s133_1 fatcat:clabpajglzb7znihy7p7ex4c4a
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