179 related articles for article (PubMed ID: 14705025)
1. Gaps in structurally similar proteins: towards improvement of multiple sequence alignment.
Wrabl JO; Grishin NV
Proteins; 2004 Jan; 54(1):71-87. PubMed ID: 14705025
[TBL] [Abstract][Full Text] [Related]
2. Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments.
Chang MS; Benner SA
J Mol Biol; 2004 Aug; 341(2):617-31. PubMed ID: 15276848
[TBL] [Abstract][Full Text] [Related]
3. A neural network method for prediction of beta-turn types in proteins using evolutionary information.
Kaur H; Raghava GP
Bioinformatics; 2004 Nov; 20(16):2751-8. PubMed ID: 15145798
[TBL] [Abstract][Full Text] [Related]
4. PROMALS: towards accurate multiple sequence alignments of distantly related proteins.
Pei J; Grishin NV
Bioinformatics; 2007 Apr; 23(7):802-8. PubMed ID: 17267437
[TBL] [Abstract][Full Text] [Related]
5. Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function.
Goonesekere NC; Lee B
Nucleic Acids Res; 2004; 32(9):2838-43. PubMed ID: 15155852
[TBL] [Abstract][Full Text] [Related]
6. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments.
Gotoh O
J Mol Biol; 1996 Dec; 264(4):823-38. PubMed ID: 8980688
[TBL] [Abstract][Full Text] [Related]
7. Variable gap penalty for protein sequence-structure alignment.
Madhusudhan MS; Marti-Renom MA; Sanchez R; Sali A
Protein Eng Des Sel; 2006 Mar; 19(3):129-33. PubMed ID: 16423846
[TBL] [Abstract][Full Text] [Related]
8. Contact-based sequence alignment.
Kleinjung J; Romein J; Lin K; Heringa J
Nucleic Acids Res; 2004; 32(8):2464-73. PubMed ID: 15121903
[TBL] [Abstract][Full Text] [Related]
9. Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence.
Kloczkowski A; Ting KL; Jernigan RL; Garnier J
Proteins; 2002 Nov; 49(2):154-66. PubMed ID: 12210997
[TBL] [Abstract][Full Text] [Related]
10. The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods.
Simossis VA; Heringa J
Comput Biol Chem; 2004 Dec; 28(5-6):351-66. PubMed ID: 15556476
[TBL] [Abstract][Full Text] [Related]
11. 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]
12. Considerations in the identification of functional RNA structural elements in genomic alignments.
Babak T; Blencowe BJ; Hughes TR
BMC Bioinformatics; 2007 Jan; 8():33. PubMed ID: 17263882
[TBL] [Abstract][Full Text] [Related]
13. Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling.
Rai BK; Fiser A
Proteins; 2006 May; 63(3):644-61. PubMed ID: 16437570
[TBL] [Abstract][Full Text] [Related]
14. Protein structure prediction begins well but ends badly.
Saunders R; Deane CM
Proteins; 2010 Apr; 78(5):1282-90. PubMed ID: 20014025
[TBL] [Abstract][Full Text] [Related]
15. Incremental window-based protein sequence alignment algorithms.
Rangwala H; Karypis G
Bioinformatics; 2007 Jan; 23(2):e17-23. PubMed ID: 17237087
[TBL] [Abstract][Full Text] [Related]
16. A simple genetic algorithm for multiple sequence alignment.
Gondro C; Kinghorn BP
Genet Mol Res; 2007 Oct; 6(4):964-82. PubMed ID: 18058716
[TBL] [Abstract][Full Text] [Related]
17. NdPASA: a novel pairwise protein sequence alignment algorithm that incorporates neighbor-dependent amino acid propensities.
Wang J; Feng JA
Proteins; 2005 Feb; 58(3):628-37. PubMed ID: 15616964
[TBL] [Abstract][Full Text] [Related]
18. A generalized affine gap model significantly improves protein sequence alignment accuracy.
Zachariah MA; Crooks GE; Holbrook SR; Brenner SE
Proteins; 2005 Feb; 58(2):329-38. PubMed ID: 15562515
[TBL] [Abstract][Full Text] [Related]
19. Improving protein secondary structure prediction with aligned homologous sequences.
Di Francesco V; Garnier J; Munson PJ
Protein Sci; 1996 Jan; 5(1):106-13. PubMed ID: 8771202
[TBL] [Abstract][Full Text] [Related]
20. Protein structure comparison by alignment of distance matrices.
Holm L; Sander C
J Mol Biol; 1993 Sep; 233(1):123-38. PubMed ID: 8377180
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]