2023
Efficient evolution of human antibodies from general protein language models
Hie B, Shanker V, Xu D, Bruun T, Weidenbacher P, Tang S, Wu W, Pak J, Kim P. Efficient evolution of human antibodies from general protein language models. Nature Biotechnology 2023, 42: 275-283. PMID: 37095349, PMCID: PMC10869273, DOI: 10.1038/s41587-023-01763-2.Peer-Reviewed Original ResearchConceptsProtein language modelsDiverse protein familiesLaboratory evolutionProtein familyProtein structureBinding specificityRare mutationsSelection pressureAntibiotic resistanceNatural evolutionary strategyEnzyme activityHuman antibodiesMature antibodiesAffinity maturationProteinAntibody bindingBinding affinityMutationsBindingEvolutionary strategyAffinityAntibodiesSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2
2022
SARS-Cov-2 variants of concern decelerate the dynamics of spike open conformation as an evolutionary strategy
Yang Z, Han Y, Ding S, Finzi A, Mothes W, Lu M. SARS-Cov-2 variants of concern decelerate the dynamics of spike open conformation as an evolutionary strategy. Biophysical Journal 2022, 121: 39a. PMCID: PMC8833081, DOI: 10.1016/j.bpj.2021.11.2500.Peer-Reviewed Original ResearchOpen conformationEvolutionary strategy
2018
Giant tortoise genomes provide insights into longevity and age-related disease
Quesada V, Freitas-Rodríguez S, Miller J, Pérez-Silva J, Jiang Z, Tapia W, Santiago-Fernández O, Campos-Iglesias D, Kuderna L, Quinzin M, Álvarez M, Carrero D, Beheregaray L, Gibbs J, Chiari Y, Glaberman S, Ciofi C, Araujo-Voces M, Mayoral P, Arango J, Tamargo-Gómez I, Roiz-Valle D, Pascual-Torner M, Evans B, Edwards D, Garrick R, Russello M, Poulakakis N, Gaughran S, Rueda D, Bretones G, Marquès-Bonet T, White K, Caccone A, López-Otín C. Giant tortoise genomes provide insights into longevity and age-related disease. Nature Ecology & Evolution 2018, 3: 87-95. PMID: 30510174, PMCID: PMC6314442, DOI: 10.1038/s41559-018-0733-x.Peer-Reviewed Original ResearchConceptsGiant tortoisesAge-related diseasesNew genome sequencesAldabra giant tortoiseDNA repair genesGiant tortoise populationLonesome GeorgeRelated speciesGenome sequenceEvolutionary informationVertebrate animalsGenomic determinantsTortoise populationsGenomeExcellent modelRepair genesCancer developmentTortoisesSupervised analysisGenesEvolutionary strategyGlobal analysisImportant resourceLast memberLongevity
2006
Nonuniform Sampling for Global Optimization of Kinetic Rate Constants in Biological Pathways
Kleinstein S, Bottino D, Georgieva A, Sarangapani R, Lett G. Nonuniform Sampling for Global Optimization of Kinetic Rate Constants in Biological Pathways. 2006, 1611-1616. DOI: 10.1109/wsc.2006.322934.Peer-Reviewed Original ResearchGlobal optimizationNon-optimal local minimaParameter estimation problemEvolutionary-type algorithmEstimation problemDifferential evolutionSlow convergenceNonuniform sampling methodLocal minimaOptimizationConvergenceEvolutionary strategyMisconvergencePowerful toolProblemPathway modelEstimationSampling methodAlgorithmRobustnessConstants
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