203 related articles for article (PubMed ID: 24307688)
1. A new formulation of protein evolutionary models that account for structural constraints.
Bordner AJ; Mittelmann HD
Mol Biol Evol; 2014 Mar; 31(3):736-49. PubMed ID: 24307688
[TBL] [Abstract][Full Text] [Related]
2. A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank.
Bastolla U; Porto M; Roman HE; Vendruscolo M
BMC Evol Biol; 2006 May; 6():43. PubMed ID: 16737532
[TBL] [Abstract][Full Text] [Related]
3. Modeling protein evolution with several amino acid replacement matrices depending on site rates.
Le SQ; Dang CC; Gascuel O
Mol Biol Evol; 2012 Oct; 29(10):2921-36. PubMed ID: 22491036
[TBL] [Abstract][Full Text] [Related]
4. An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation.
Wang HC; Susko E; Roger AJ
Mol Biol Evol; 2014 Apr; 31(4):779-92. PubMed ID: 24441033
[TBL] [Abstract][Full Text] [Related]
5. Assessing site-interdependent phylogenetic models of sequence evolution.
Rodrigue N; Philippe H; Lartillot N
Mol Biol Evol; 2006 Sep; 23(9):1762-75. PubMed ID: 16787998
[TBL] [Abstract][Full Text] [Related]
6. What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood.
Lakner C; Holder MT; Goldman N; Naylor GJ
Syst Biol; 2011 Mar; 60(2):161-74. PubMed ID: 21233085
[TBL] [Abstract][Full Text] [Related]
7. Site interdependence attributed to tertiary structure in amino acid sequence evolution.
Rodrigue N; Lartillot N; Bryant D; Philippe H
Gene; 2005 Mar; 347(2):207-17. PubMed ID: 15733531
[TBL] [Abstract][Full Text] [Related]
8. A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution.
Chi PB; Kim D; Lai JK; Bykova N; Weber CC; Kubelka J; Liberles DA
Proteins; 2018 Feb; 86(2):218-228. PubMed ID: 29178386
[TBL] [Abstract][Full Text] [Related]
9. Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability.
Arenas M; Sánchez-Cobos A; Bastolla U
Mol Biol Evol; 2015 Aug; 32(8):2195-207. PubMed ID: 25837579
[TBL] [Abstract][Full Text] [Related]
10. Empirical models for substitution in ribosomal RNA.
Smith AD; Lui TW; Tillier ER
Mol Biol Evol; 2004 Mar; 21(3):419-27. PubMed ID: 14660689
[TBL] [Abstract][Full Text] [Related]
11. Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes.
Parisi G; Echave J
Gene; 2005 Jan; 345(1):45-53. PubMed ID: 15716088
[TBL] [Abstract][Full Text] [Related]
12. Improving phylogenetic inference with a semiempirical amino acid substitution model.
Zoller S; Schneider A
Mol Biol Evol; 2013 Feb; 30(2):469-79. PubMed ID: 23002090
[TBL] [Abstract][Full Text] [Related]
13. A site- and time-heterogeneous model of amino acid replacement.
Blanquart S; Lartillot N
Mol Biol Evol; 2008 May; 25(5):842-58. PubMed ID: 18234708
[TBL] [Abstract][Full Text] [Related]
14. Evolutionary patterns in coiled-coils.
Surkont J; Pereira-Leal JB
Genome Biol Evol; 2015 Jan; 7(2):545-56. PubMed ID: 25577198
[TBL] [Abstract][Full Text] [Related]
15. A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor.
Brooks DJ; Fresco JR; Singh M
Bioinformatics; 2004 Sep; 20(14):2251-7. PubMed ID: 15073018
[TBL] [Abstract][Full Text] [Related]
16. A transition probability model for amino acid substitutions from blocks.
Veerassamy S; Smith A; Tillier ER
J Comput Biol; 2003; 10(6):997-1010. PubMed ID: 14980022
[TBL] [Abstract][Full Text] [Related]
17. Statistical potentials for improved structurally constrained evolutionary models.
Kleinman CL; Rodrigue N; Lartillot N; Philippe H
Mol Biol Evol; 2010 Jul; 27(7):1546-60. PubMed ID: 20159780
[TBL] [Abstract][Full Text] [Related]
18. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes.
Yang Z; Swanson WJ
Mol Biol Evol; 2002 Jan; 19(1):49-57. PubMed ID: 11752189
[TBL] [Abstract][Full Text] [Related]
19. Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account.
Mayrose I; Mitchell A; Pupko T
J Mol Evol; 2005 Mar; 60(3):345-53. PubMed ID: 15871045
[TBL] [Abstract][Full Text] [Related]
20. Relating physicochemical properties of amino acids to variable nucleotide substitution patterns among sites.
Yang Z
Pac Symp Biocomput; 2000; ():81-92. PubMed ID: 10902158
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
