These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
23. Protein homology detection by HMM-HMM comparison. Söding J Bioinformatics; 2005 Apr; 21(7):951-60. PubMed ID: 15531603 [TBL] [Abstract][Full Text] [Related]
24. Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST. Goonesekere NC Adv Appl Bioinform Chem; 2009; 2():71-8. PubMed ID: 21918617 [TBL] [Abstract][Full Text] [Related]
25. dRHP-PseRA: detecting remote homology proteins using profile-based pseudo protein sequence and rank aggregation. Chen J; Long R; Wang XL; Liu B; Chou KC Sci Rep; 2016 Sep; 6():32333. PubMed ID: 27581095 [TBL] [Abstract][Full Text] [Related]
26. Significant speedup of database searches with HMMs by search space reduction with PSSM family models. Beckstette M; Homann R; Giegerich R; Kurtz S Bioinformatics; 2009 Dec; 25(24):3251-8. PubMed ID: 19828575 [TBL] [Abstract][Full Text] [Related]
27. The effectiveness of position- and composition-specific gap costs for protein similarity searches. Stojmirović A; Gertz EM; Altschul SF; Yu YK Bioinformatics; 2008 Jul; 24(13):i15-23. PubMed ID: 18586708 [TBL] [Abstract][Full Text] [Related]
28. HH-suite3 for fast remote homology detection and deep protein annotation. Steinegger M; Meier M; Mirdita M; Vöhringer H; Haunsberger SJ; Söding J BMC Bioinformatics; 2019 Sep; 20(1):473. PubMed ID: 31521110 [TBL] [Abstract][Full Text] [Related]
29. Large-scale comparison of protein sequence alignment algorithms with structure alignments. Sauder JM; Arthur JW; Dunbrack RL Proteins; 2000 Jul; 40(1):6-22. PubMed ID: 10813826 [TBL] [Abstract][Full Text] [Related]
30. A comparison of position-specific score matrices based on sequence and structure alignments. Panchenko AR; Bryant SH Protein Sci; 2002 Feb; 11(2):361-70. PubMed ID: 11790846 [TBL] [Abstract][Full Text] [Related]
31. Distant homology detection using a LEngth and STructure-based sequence Alignment Tool (LESTAT). Lee MM; Bundschuh R; Chan MK Proteins; 2008 May; 71(3):1409-19. PubMed ID: 18076050 [TBL] [Abstract][Full Text] [Related]
32. Effective detection of remote homologues by searching in sequence dataset of a protein domain fold. Sandhya S; Kishore S; Sowdhamini R; Srinivasan N FEBS Lett; 2003 Sep; 552(2-3):225-30. PubMed ID: 14527691 [TBL] [Abstract][Full Text] [Related]
33. Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. Schmidt Am Busch M; Sedano A; Simonson T PLoS One; 2010 May; 5(5):e10410. PubMed ID: 20463972 [TBL] [Abstract][Full Text] [Related]
38. Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. Wallqvist A; Fukunishi Y; Murphy LR; Fadel A; Levy RM Bioinformatics; 2000 Nov; 16(11):988-1002. PubMed ID: 11159310 [TBL] [Abstract][Full Text] [Related]
39. Application of learning to rank to protein remote homology detection. Liu B; Chen J; Wang X Bioinformatics; 2015 Nov; 31(21):3492-8. PubMed ID: 26163693 [TBL] [Abstract][Full Text] [Related]