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Journal Abstract Search

119 related items for PubMed ID: 12821306

  • 1. Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution.
    Lin K, Kleinjung J, Taylor WR, Heringa J.
    Comput Biol Chem; 2003 May; 27(2):93-102. PubMed ID: 12821306
    [Abstract] [Full Text] [Related]

  • 2. Contact-based sequence alignment.
    Kleinjung J, Romein J, Lin K, Heringa J.
    Nucleic Acids Res; 2004 May; 32(8):2464-73. PubMed ID: 15121903
    [Abstract] [Full Text] [Related]

  • 3. Contact-based Simulated Annealing Protein Sequence Alignment Method.
    Dong QW, Lin L, Wang XL, Li MH.
    Conf Proc IEEE Eng Med Biol Soc; 2005 May; 2005():2798-801. PubMed ID: 17282823
    [Abstract] [Full Text] [Related]

  • 4. Non-Markovian effects on protein sequence evolution due to site dependent substitution rates.
    Rizzato F, Rodriguez A, Laio A.
    BMC Bioinformatics; 2016 Jun 24; 17():258. PubMed ID: 27342318
    [Abstract] [Full Text] [Related]

  • 5. PASS2: an automated database of protein alignments organised as structural superfamilies.
    Bhaduri A, Pugalenthi G, Sowdhamini R.
    BMC Bioinformatics; 2004 Apr 02; 5():35. PubMed ID: 15059245
    [Abstract] [Full Text] [Related]

  • 6. Amino acid similarity matrix for homology modeling derived from structural alignment and optimized by the Monte Carlo method.
    Ogata K, Ohya M, Umeyama H.
    J Mol Graph Model; 1998 Apr 02; 16(4-6):178-89, 254. PubMed ID: 10522237
    [Abstract] [Full Text] [Related]

  • 7. Bayesian coestimation of phylogeny and sequence alignment.
    Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.
    BMC Bioinformatics; 2005 Apr 01; 6():83. PubMed ID: 15804354
    [Abstract] [Full Text] [Related]

  • 8. The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs.
    Griffiths-Jones S, Bateman A.
    Bioinformatics; 2002 Sep 01; 18(9):1243-9. PubMed ID: 12217916
    [Abstract] [Full Text] [Related]

  • 9. A transition probability model for amino acid substitutions from blocks.
    Veerassamy S, Smith A, Tillier ER.
    J Comput Biol; 2003 Sep 01; 10(6):997-1010. PubMed ID: 14980022
    [Abstract] [Full Text] [Related]

  • 10. Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions.
    Huang YM, Bystroff C.
    Bioinformatics; 2006 Feb 15; 22(4):413-22. PubMed ID: 16352653
    [Abstract] [Full Text] [Related]

  • 11. Amino acid substitution during functionally constrained divergent evolution of protein sequences.
    Benner SA, Cohen MA, Gonnet GH.
    Protein Eng; 1994 Nov 15; 7(11):1323-32. PubMed ID: 7700864
    [Abstract] [Full Text] [Related]

  • 12. A Mutation Model from First Principles of the Genetic Code.
    Thorvaldsen S.
    IEEE/ACM Trans Comput Biol Bioinform; 2016 Nov 15; 13(5):878-886. PubMed ID: 26485722
    [Abstract] [Full Text] [Related]

  • 13. A new criterion and method for amino acid classification.
    Kosiol C, Goldman N, Buttimore NH.
    J Theor Biol; 2004 May 07; 228(1):97-106. PubMed ID: 15064085
    [Abstract] [Full Text] [Related]

  • 14. Are residues in a protein folding nucleus evolutionarily conserved?
    Tseng YY, Liang J.
    J Mol Biol; 2004 Jan 23; 335(4):869-80. PubMed ID: 14698285
    [Abstract] [Full Text] [Related]

  • 15. QUASAR--scoring and ranking of sequence-structure alignments.
    Birzele F, Gewehr JE, Zimmer R.
    Bioinformatics; 2005 Dec 15; 21(24):4425-6. PubMed ID: 16216828
    [Abstract] [Full Text] [Related]

  • 16. Modeling amino acid replacement.
    Müller T, Vingron M.
    J Comput Biol; 2000 Dec 15; 7(6):761-76. PubMed ID: 11382360
    [Abstract] [Full Text] [Related]

  • 17. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.
    Tan YH, Huang H, Kihara D.
    Proteins; 2006 Aug 15; 64(3):587-600. PubMed ID: 16799934
    [Abstract] [Full Text] [Related]

  • 18. Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins.
    Yuan X, Bystroff C.
    Bioinformatics; 2005 Apr 01; 21(7):1010-9. PubMed ID: 15531601
    [Abstract] [Full Text] [Related]

  • 19. Simultaneous sequence alignment and tree construction using hidden Markov models.
    Edgar RC, Sjölander K.
    Pac Symp Biocomput; 2003 Apr 01; ():180-91. PubMed ID: 12603027
    [Abstract] [Full Text] [Related]

  • 20. Hidden Markov models of biological primary sequence information.
    Baldi P, Chauvin Y, Hunkapiller T, McClure MA.
    Proc Natl Acad Sci U S A; 1994 Feb 01; 91(3):1059-63. PubMed ID: 8302831
    [Abstract] [Full Text] [Related]

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