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Beyond Mutation Matrices: Physical-Chemistry Based Evolutionary Models

Jeffrey M. Koshi, David P. Mindell, Richard A. Goldstein
1997 Genome Informatics Series  
By representing the fitness of each of the amino acids as a function of the physical-chemical properties of that amino acid, and constructing mutation matrices based on Boltzmann statistics and Metropolis  ...  We describe a model for characterizing site mutations in evolving proteins.  ...  Acknowledgments We would like to thank Darin Taverna for his work in deriving the the models of amino acid substitution used in this work.  ... 
doi:10.11234/gi1990.8.80 fatcat:tcjya6zyujcjpkvmyxgyxa3bmi

Beyond mutation matrices

Jeffrey M. Koshi, David P. Mindell, Richard A. Goldstein
1998 Proceedings of the second annual international conference on Computational molecular biology - RECOMB '98  
By representing the tness of each of the amino acids as a function of the physical-chemical properties of that amino acid, and constructing mutation matrices based on Boltzmann statistics and Metropolis  ...  We describe a m o del for characterizing site mutations in evolving proteins.  ...  Acknowledgments We w ould like to thank Darin Taverna for his work in deriving the the models of amino acid substitution used in this work.  ... 
doi:10.1145/279069.279107 dblp:conf/recomb/KoshiMG98 fatcat:u2vv5ipxvnczdh2hzpa4ub4llq

Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes

J. M. Koshi, D. P. Mindell, R. A. Goldstein
1999 Molecular biology and evolution  
This model, based on Boltzmann statistics and Metropolis kinetics, involves an order of magnitude fewer adjustable parameters than traditional substitution matrices and deals more effectively with the  ...  When optimized for sequences of HIV-1 envelope (env) proteins from a few specific subtypes, our model is more likely to describe the evolutionary record for other subtypes than are methods using a single  ...  Construction of Physical-Chemistry-Based Substitution Matrices With 20 different amino acids, the complete specification of a substitution matrix would require the determination of 380 adjustable parameters  ... 
doi:10.1093/oxfordjournals.molbev.a026100 pmid:10028285 fatcat:xkdr2kzdpvfftfanrjjgsratla

Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes

A JUSTE, B THOMMA, B LIEVENS
2008 Food microbiology  
Limitations associated with traditional culture-based methods have pushed for the development of culture-independent techniques, which are primarily based on the analysis of nucleic acids.  ...  It is unlikely that a single approach will be universally applicable for analyzing microbial communities in unknown matrices.  ...  Storing thick juice beyond extraction and refining is common practice in the sugar industry.  ... 
doi:10.1016/j.fm.2008.04.009 pmid:18620966 fatcat:ll6s5zdf3begbckowygiwgzvyq

The Evolution of Protein Structures and Structural Ensembles Under Functional Constraint

Jessica Siltberg-Liberles, Johan A. Grahnen, David A. Liberles
2011 Genes  
Lastly, a brief discussion of modeling the evolution of sequences of ordered and disordered proteins is entertained.  ...  Moving beyond static structures, the evolution of protein kinetics (including normal modes) is discussed, as is the evolution of conformational ensembles and structurally disordered proteins.  ...  As our understanding of protein sequence-structure links and the intertwining roles of physical chemistry and evolution improves, key aspects of our knowledge based on protein structural evolution may  ... 
doi:10.3390/genes2040748 pmid:24710290 pmcid:PMC3927589 fatcat:khnpkvulljd47nteu775ibo6j4

Can all heritable biology really be reduced to a single dimension?

Gregory A. Babbitt, Erin E. Coppola, Mohammed A. Alawad, André O. Hudson
2016 Gene  
We review a selection of new bioinformatic methods that move beyond sequence-based approaches to include consideration of databased three dimensional structures.  ...  This static model of DNA led very quickly to the conclusion that only the nucleobase sequence itself is rich enough in molecular complexity to replicate a complex biology.  ...  Recent findings of structural-based biases in mutational processes regarding DNA (Babbitt and Schulze, 2012; Babbitt et al., 2014) , RNA (Chamary and Hurst, 2005) and even DNA's physical interactions  ... 
doi:10.1016/j.gene.2015.12.043 pmid:26723512 fatcat:eeil2pzdwrga3dj6r24da4pezi

Evolutionary predictions of binding surfaces and interactions

Olivier Lichtarge, Mathew E Sowa
2002 Current Opinion in Structural Biology  
Abbreviations ET evolutionary trace G α α G protein α subunit HMM hidden Markov model IR intracellular hormone receptor MSA multiple sequence alignment PDB Protein Data Bank RGS regulator of G protein  ...  Thus, the effective functional site not only includes part of the ligand contact site, but also extends beyond it through allosteric interactions, and the effect of specific mutations depends largely on  ...  Recent variations on this basic scheme add quantitative descriptions of residue variability (weighted evolutionary tracing [36] ), use amino acid exchange matrices to better tolerate variations within  ... 
doi:10.1016/s0959-440x(02)00284-1 pmid:11839485 fatcat:277tafwkv5bxzc736ybktlm3ya

Towards a Framework for Observing Artificial Evolutionary Systems [article]

Janardan Misra
2009 arXiv   pre-print
The examples of Cellular Automata based Langton Loops and Lambda calculus based Algorithmic Chemistry are used to illustrate the framework.  ...  that must be met in order to establish the level of evolutionary behavior in the model.  ...  Langton defined in [Lan90] a quantitative matric, called lambda parameter to detect life in any generic one dimensional cellular automata model based upon the characteristics of its transition rules.  ... 
arXiv:0901.1610v1 fatcat:mlledjtybzb63khnvgrisiit7m

Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-Modular Coupling

Charles Carter, Alex Popinga, Remco Bouckaert, Peter Wills
2022 International Journal of Molecular Sciences  
We seek evidence about their ancestry from curated structure-based multiple sequence alignments of a structurally invariant "scaffold" shared by all 10 canonical Class I aaRS.  ...  Three uncorrelated phylogenetic metrics—mutation frequency, its uniformity, and row-by-row cladistic congruence—imply that the Class I scaffold is a mosaic assembled from successive genetic sources.  ...  on empirical substitution matrices and estimates of relative rates of mutation [63] .  ... 
doi:10.3390/ijms23031520 pmid:35163448 pmcid:PMC8835825 fatcat:ouqejyfemnedhdhsh3u4eznuxq

Glycan Evolution in Response to Collaboration, Conflict, and Constraint

Stevan A. Springer, Pascal Gagneux
2013 Journal of Biological Chemistry  
Robustness is the ability of a phenotype to tolerate evolutionary change and thus explore new functions by mutation (9).  ...  For evolutionary biologists, glycans are an opportunity to test models of behavioral evolution on mechanistically tractable phenotypes (2) .  ...  We adopt a classification based on the elements that come into evolutionary conflict (the phenotypes of single alleles or multiple genes) and the arena in which conflict plays out (how these phenotypes  ... 
doi:10.1074/jbc.r112.424523 pmid:23329843 pmcid:PMC3591600 fatcat:kf3rcn6dnra3fdr2b75h5h7wzi

The major synthetic evolutionary transitions

Ricard Solé
2016 Philosophical Transactions of the Royal Society of London. Biological Sciences  
Evolved, autonomous entities capable of replicating or reproducing [5] and being the subject of selection must have been to some extent capable of moving beyond non-living chemistry to a novel form of  ...  Replicators, viruses and protocells The origins of early replicators and the first protocellular systems are necessarily closer to physics and systems chemistry than any other MET.  ... 
doi:10.1098/rstb.2016.0175 pmid:27431528 pmcid:PMC4958944 fatcat:3b2kfj75ebes7jutanegaiapsq

Genetic algorithms in astronomy and astrophysics [article]

Vinesh Rajpaul
2012 arXiv   pre-print
GA-based optimisers tend to be extremely robust and versatile compared to most traditional techniques used to solve optimisation problems.  ...  The same holds true for the all-important inverse problems that are ubiquitous in the physical sciences, i.e. problems where one seeks to transform experimental data into model parameters in order infer  ...  The widespread adoption of GAs in fields such as engineering, chemistry, biology and economics bears testimony to their great versatility [3] .  ... 
arXiv:1202.1643v1 fatcat:xqzonhfbgrdcplserqqovxakjy

Evolution of metabolic networks: a computational frame-work

Christoph Flamm, Alexander Ullrich, Heinz Ekker, Martin Mann, Daniel Högerl, Markus Rohrschneider, Sebastian Sauer, Gerik Scheuermann, Konstantin Klemm, Ivo L Hofacker, Peter F Stadler
2010 Journal of Systems Chemistry  
We employ an artificial chemistry that views chemical reactions as graph rewriting operations and utilizes a toy-version of quantum chemistry to derive thermodynamic parameters.  ...  Minimalist organisms with simple string-encoded genomes produce model ribozymes whose catalytic activity is determined by an ad hoc mapping between their secondary structure and the transition state graphs  ...  I/ 82719, and the COST-Action CM0703 "Systems Chemistry".  ... 
doi:10.1186/1759-2208-1-4 fatcat:pa2utwth3zdfnbib3zuujdgwxm

Class I Aminoacyl-tRNA Synthetase Urzyme and CP1 Modules have Distinct Genetic Origins [article]

Charles W Carter, Alex Popinga, Remco Bouckaert, Peter Wills
2020 bioRxiv   pre-print
This work represents the first time that i) sophisticated structure-based alignment has been used to curate multiple sequence alignments identifying what is conserved across an entire protein superfamily  ...  As each new, refined amino acid type emerged, all extant gene sequences 392 adapted to opportunities introduced by progressively finer discrimination between amino acid side 393 chain physical chemistry  ...  A parallel sub-classification in Class II aaRS 78 strengthens connections [11-13] between Class I and II phylogenies and the physical chemistry 79 differentiating the 10 amino acids in each Class. 80 Three  ... 
doi:10.1101/2020.04.09.033712 fatcat:wlrhuy7m7jc7lkfxnacy25ofqq

Evolving Reaction-Diffusion Systems on GPU [chapter]

Lidia Yamamoto, Wolfgang Banzhaf, Pierre Collet
2011 Lecture Notes in Computer Science  
Reaction-diffusion systems contribute to various morphogenetic processes, and can also be used as computation models in real and artificial chemistries.  ...  Our results indicate that these two optimization modes tend to exhibit qualitatively different evolutionary dynamics: in the former, the fitness tends to improve continuously in gentle slopes, while the  ...  A GP-based approach to RD evolution covers a much larger search space than a GA-based one.  ... 
doi:10.1007/978-3-642-24769-9_16 fatcat:k253x5z77vapthpagqkt3gb4qq
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