Simulation of protein evolution along phylogenies under structure-based substitution models Long Description (required)
ProteinEvolver generates samples of protein-coding genes and protein sequences evolved along phylogenies under structure-based substitution models. These models consider the protein structure to evaluate candidate mutations, which can be accepted (substitutions) or rejected depending on the energy of the protein structure of the mutated sequence. The simulation of molecular evolution occurs along phylogenetic histories, which can be either user-specified or simulated by the coalescent modified with recombination (including recombination hotspots), migration, demographics and longitudinal sampling. http://code.google.com/p/proteinevolver/ miguelmmmab@gmail.com
Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.
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Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s).
Can't Find the Attribute You Are Looking For? If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab .
Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 24037213 ],
Arenas M, Dos Santos HG, Posada D, Bastolla U ,
Protein evolution along phylogenetic histories under structurally constrained substitution models. ,
Bioinformatics ,
12-01-2013 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=24037213, Primary Citation
[Pubmed ID: 30958823 ],
Facco E, Pagnani A, Russo ET, Laio A ,
The intrinsic dimension of protein sequence evolution. ,
PLoS Comput Biol ,
04-08-2019 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=30958823, , Application
[Pubmed ID: 36463317 ],
Del Amparo R, González-Vázquez LD, Rodríguez-Moure L, Bastolla U, Arenas M ,
Consequences of Genetic Recombination on Protein Folding Stability. ,
J Mol Evol ,
02-01-2023 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=36463317, , Application