@article {677,
	title = {ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.},
	journal = {Nucleic Acids Res},
	volume = {38},
	year = {2010},
	month = {2010 Jul},
	pages = {W529-33},
	abstract = {It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionary conservation of amino acid positions in proteins using an empirical Bayesian inference, starting from protein structure and sequence, respectively. Here, we present the new version of the ConSurf web server that combines the two independent servers, providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process. In addition, the new version of ConSurf calculates the evolutionary rates for nucleic acid sequences. The new version is freely available at: http://consurf.tau.ac.il/.},
	keywords = {Amino Acid Sequence, Base Sequence, Conserved Sequence, Evolution, Molecular, Internet, Nucleic Acid Conformation, Protein Conformation, Sequence Analysis, Sequence Homology, Amino Acid, Software},
	issn = {1362-4962},
	doi = {10.1093/nar/gkq399},
	author = {Ashkenazy, Haim and Erez, Elana and Martz, Eric and Pupko, Tal and Ben-Tal, Nir}
}
@article {682,
	title = {Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.},
	journal = {Nucleic Acids Res},
	volume = {35},
	year = {2007},
	month = {2007 Jul},
	pages = {W506-11},
	abstract = {Biologically significant sites in a protein may be identified by contrasting the rates of synonymous (K(s)) and non-synonymous (K(a)) substitutions. This enables the inference of site-specific positive Darwinian selection and purifying selection. We present here Selecton version 2.2 (http://selecton.bioinfo.tau.ac.il), a web server which automatically calculates the ratio between K(a) and K(s) (omega) at each site of the protein. This ratio is graphically displayed on each site using a color-coding scheme, indicating either positive selection, purifying selection or lack of selection. Selecton implements an assembly of different evolutionary models, which allow for statistical testing of the hypothesis that a protein has undergone positive selection. Specifically, the recently developed mechanistic-empirical model is introduced, which takes into account the physicochemical properties of amino acids. Advanced options were introduced to allow maximal fine tuning of the server to the user{\textquoteright}s specific needs, including calculation of statistical support of the omega values, an advanced graphic display of the protein{\textquoteright}s 3-dimensional structure, use of different genetic codes and inputting of a pre-built phylogenetic tree. Selecton version 2.2 is an effective, user-friendly and freely available web server which implements up-to-date methods for computing site-specific selection forces, and the visualization of these forces on the protein{\textquoteright}s sequence and structure.},
	keywords = {Algorithms, Amino Acid Sequence, Amino Acid Substitution, Amino Acids, Animals, Bayes Theorem, Computational Biology, Computer Simulation, Humans, Internet, Models, Molecular, Molecular Sequence Data, Phylogeny, Proteins, Sequence Analysis, Protein, Software},
	issn = {1362-4962},
	doi = {10.1093/nar/gkm382},
	author = {Stern, Adi and Doron-Faigenboim, Adi and Erez, Elana and Martz, Eric and Bacharach, Eran and Pupko, Tal}
}
