2024
Fast, sensitive detection of protein homologs using deep dense retrieval
Hong L, Hu Z, Sun S, Tang X, Wang J, Tan Q, Zheng L, Wang S, Xu S, King I, Gerstein M, Li Y. Fast, sensitive detection of protein homologs using deep dense retrieval. Nature Biotechnology 2024, 1-13. PMID: 39123049, DOI: 10.1038/s41587-024-02353-6.Peer-Reviewed Original ResearchProtein language modelsRemote homologsProtein homologsProtein sequence comparisonsAlignment-based approachesWell-characterized proteinsPSI-BLASTSuperfamily levelProtein evolutionSequence comparisonProtein sequencesHomologyProteinSensitivity compared to previous methodsSensitive detectionHMMERSuperfamilyStructural informationSequence
2005
Calculation of Standard Atomic Volumes for RNA and Comparison with Proteins: RNA is Packed More Tightly
Voss NR, Gerstein M. Calculation of Standard Atomic Volumes for RNA and Comparison with Proteins: RNA is Packed More Tightly. Journal Of Molecular Biology 2005, 346: 477-492. PMID: 15670598, DOI: 10.1016/j.jmb.2004.11.072.Peer-Reviewed Original Research