109 related articles for article (PubMed ID: 11694178)
21. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence.
Rice DW; Eisenberg D
J Mol Biol; 1997 Apr; 267(4):1026-38. PubMed ID: 9135128
[TBL] [Abstract][Full Text] [Related]
22. A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins.
Brick K; Pizzi E
BMC Bioinformatics; 2008 May; 9():236. PubMed ID: 18485187
[TBL] [Abstract][Full Text] [Related]
23. Comparison of the PAM and BLOSUM Amino Acid Substitution Matrices.
Mount DW
CSH Protoc; 2008 Jun; 2008():pdb.ip59. PubMed ID: 21356840
[TBL] [Abstract][Full Text] [Related]
24. Genome bias influences amino acid choices: analysis of amino acid substitution and re-compilation of substitution matrices exclusive to an AT-biased genome.
Paila U; Kondam R; Ranjan A
Nucleic Acids Res; 2008 Dec; 36(21):6664-75. PubMed ID: 18948281
[TBL] [Abstract][Full Text] [Related]
25. Performance evaluation of amino acid substitution matrices.
Henikoff S; Henikoff JG
Proteins; 1993 Sep; 17(1):49-61. PubMed ID: 8234244
[TBL] [Abstract][Full Text] [Related]
26. Using BLOSUM in Sequence Alignments.
Mount DW
CSH Protoc; 2008 Jun; 2008():pdb.top39. PubMed ID: 21356855
[TBL] [Abstract][Full Text] [Related]
27. Amino acid "little Big Bang": representing amino acid substitution matrices as dot products of Euclidian vectors.
Zimmermann K; Gibrat JF
BMC Bioinformatics; 2010 Jan; 11():4. PubMed ID: 20047649
[TBL] [Abstract][Full Text] [Related]
28. 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]
29. SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment.
Barlowe S; Coan HB; Youker RT
PeerJ; 2017; 5():e3492. PubMed ID: 28674656
[TBL] [Abstract][Full Text] [Related]
30. Depth dependent amino acid substitution matrices and their use in predicting deleterious mutations.
Farheen N; Sen N; Nair S; Tan KP; Madhusudhan MS
Prog Biophys Mol Biol; 2017 Sep; 128():14-23. PubMed ID: 28212855
[TBL] [Abstract][Full Text] [Related]
31. Estimation of amino acid residue substitution rates at local spatial regions and application in protein function inference: a Bayesian Monte Carlo approach.
Tseng YY; Liang J
Mol Biol Evol; 2006 Feb; 23(2):421-36. PubMed ID: 16251508
[TBL] [Abstract][Full Text] [Related]
32. Neural network-based prediction of mutation-induced protein stability changes in Staphylococcal nuclease at 20 residue positions.
Frenz CM
Proteins; 2005 May; 59(2):147-51. PubMed ID: 15723345
[TBL] [Abstract][Full Text] [Related]
33. EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments.
Gelly JC; Chiche L; Gracy J
BMC Bioinformatics; 2005 Jan; 6():4. PubMed ID: 15638949
[TBL] [Abstract][Full Text] [Related]
34. Prediction of protein secondary structure content using amino acid composition and evolutionary information.
Lee S; Lee BC; Kim D
Proteins; 2006 Mar; 62(4):1107-14. PubMed ID: 16345074
[TBL] [Abstract][Full Text] [Related]
35. Selecting the Right Similarity-Scoring Matrix.
Pearson WR
Curr Protoc Bioinformatics; 2013; 43():3.5.1-3.5.9. PubMed ID: 24509512
[TBL] [Abstract][Full Text] [Related]
36. 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]
37. An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited.
Vogt G; Etzold T; Argos P
J Mol Biol; 1995 Jun; 249(4):816-31. PubMed ID: 7602593
[TBL] [Abstract][Full Text] [Related]
38. PSSM-based prediction of DNA binding sites in proteins.
Ahmad S; Sarai A
BMC Bioinformatics; 2005 Feb; 6():33. PubMed ID: 15720719
[TBL] [Abstract][Full Text] [Related]
39. Inconsistent distances in substitution matrices can be avoided by properly handling hydrophobic residues.
Baussand J; Carbone A
Evol Bioinform Online; 2008 Oct; 4():255-61. PubMed ID: 19204823
[TBL] [Abstract][Full Text] [Related]
40. Enriching the sequence substitution matrix by structural information.
Teodorescu O; Galor T; Pillardy J; Elber R
Proteins; 2004 Jan; 54(1):41-8. PubMed ID: 14705022
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]