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.
159 related articles for article (PubMed ID: 37725369)
21. Embeddings from protein language models predict conservation and variant effects. Marquet C; Heinzinger M; Olenyi T; Dallago C; Erckert K; Bernhofer M; Nechaev D; Rost B Hum Genet; 2022 Oct; 141(10):1629-1647. PubMed ID: 34967936 [TBL] [Abstract][Full Text] [Related]
22. Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences. Hauswedell H; Hetzel S; Gottlieb SG; Kretzmer H; Meissner A; Reinert K Bioinformatics; 2024 Mar; 40(3):. PubMed ID: 38485699 [TBL] [Abstract][Full Text] [Related]
23. 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]
24. Finding Similar Nucleotide Sequences Using Network BLAST Searches. Ladunga I Curr Protoc Bioinformatics; 2017 Jun; 58():3.3.1-3.3.25. PubMed ID: 28654728 [TBL] [Abstract][Full Text] [Related]
25. Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone. Pantolini L; Studer G; Pereira J; Durairaj J; Tauriello G; Schwede T Bioinformatics; 2024 Jan; 40(1):. PubMed ID: 38175775 [TBL] [Abstract][Full Text] [Related]
26. Sensitive remote homology search by local alignment of small positional embeddings from protein language models. Johnson SR; Peshwa M; Sun Z Elife; 2024 Mar; 12():. PubMed ID: 38488154 [TBL] [Abstract][Full Text] [Related]
27. Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under MICROSOFT WINDOWS 95/NT. Durand P; Canard L; Mornon JP Comput Appl Biosci; 1997 Aug; 13(4):407-13. PubMed ID: 9283755 [TBL] [Abstract][Full Text] [Related]
28. FusOn-pLM: A Fusion Oncoprotein-Specific Language Model via Focused Probabilistic Masking. Vincoff S; Goel S; Kholina K; Pulugurta R; Vure P; Chatterjee P bioRxiv; 2024 Jun; ():. PubMed ID: 38895377 [TBL] [Abstract][Full Text] [Related]
30. Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Li W; Pio F; Pawłowski K; Godzik A Bioinformatics; 2000 Dec; 16(12):1105-10. PubMed ID: 11159329 [TBL] [Abstract][Full Text] [Related]
31. COMPASS server for remote homology inference. Sadreyev RI; Tang M; Kim BH; Grishin NV Nucleic Acids Res; 2007 Jul; 35(Web Server issue):W653-8. PubMed ID: 17517780 [TBL] [Abstract][Full Text] [Related]
32. Database indexing for production MegaBLAST searches. Morgulis A; Coulouris G; Raytselis Y; Madden TL; Agarwala R; Schäffer AA Bioinformatics; 2008 Aug; 24(16):1757-64. PubMed ID: 18567917 [TBL] [Abstract][Full Text] [Related]
33. ManyFold: an efficient and flexible library for training and validating protein folding models. Villegas-Morcillo A; Robinson L; Flajolet A; Barrett TD Bioinformatics; 2023 Jan; 39(1):. PubMed ID: 36495196 [TBL] [Abstract][Full Text] [Related]
34. Portable BLAST-like algorithm library and its implementations for command line, Python, and R. Schmid S; Jeevannavar A; Julian TR; Tamminen M PLoS One; 2023; 18(11):e0289693. PubMed ID: 38032878 [TBL] [Abstract][Full Text] [Related]
35. FastBLAST: homology relationships for millions of proteins. Price MN; Dehal PS; Arkin AP PLoS One; 2008; 3(10):e3589. PubMed ID: 18974889 [TBL] [Abstract][Full Text] [Related]
36. MAFFT-DASH: integrated protein sequence and structural alignment. Rozewicki J; Li S; Amada KM; Standley DM; Katoh K Nucleic Acids Res; 2019 Jul; 47(W1):W5-W10. PubMed ID: 31062021 [TBL] [Abstract][Full Text] [Related]
37. 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]
38. The HHpred interactive server for protein homology detection and structure prediction. Söding J; Biegert A; Lupas AN Nucleic Acids Res; 2005 Jul; 33(Web Server issue):W244-8. PubMed ID: 15980461 [TBL] [Abstract][Full Text] [Related]
39. S-PLM: Structure-aware Protein Language Model via Contrastive Learning between Sequence and Structure. Wang D; Pourmirzaei M; Abbas UL; Zeng S; Manshour N; Esmaili F; Poudel B; Jiang Y; Shao Q; Chen J; Xu D bioRxiv; 2024 May; ():. PubMed ID: 37609352 [TBL] [Abstract][Full Text] [Related]
40. Finding Homologs in Amino Acid Sequences Using Network BLAST Searches. Ladunga I Curr Protoc Bioinformatics; 2017 Sep; 59():3.4.1-3.4.24. PubMed ID: 28902395 [TBL] [Abstract][Full Text] [Related] [Previous] [Next] [New Search]