Novel methods for multiple sequence alignment and evolutionary modeling

Συγγραφείς: Mansouri, Leila

Συνεισφορές: University/Department: Universitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida

Thesis Advisors: Notredame, Cedric

Πηγή: TDX (Tesis Doctorals en Xarxa)

Θεματικοί όροι: Alineamiento de secuencias múltiples, AlphaFold2, Filogenia, Estructura de proteínas, Evolución de proteínas, Multiple Sequence alignment, Phylogeny, Structure of protein, Protein evolution

Περιγραφή αρχείου: application/pdf

Σύνδεσμος πρόσβασης: http://hdl.handle.net/10803/688007

Structural Basis for Nucleobase Activation by the Adenine DNA Glycosylase MutY

Συγγραφείς: Russelburg, L Peyton, Demir, Merve, Cedeno, Karina, David, Sheila S, Horvath, Martin P

Πηγή: ChemBioChem. 27(11)

Θεματικοί όροι: 3101 Biochemistry and Cell Biology (for-2020), 31 Biological Sciences (for-2020), Cancer (rcdc), DNA Glycosylases (mesh), Geobacillus stearothermophilus (mesh), Crystallography, X-Ray (mesh), Adenine (mesh), Models, Molecular (mesh), Guanine (mesh), Kinetics (mesh), Adenine (mesh), Guanine (mesh), DNA Glycosylases (mesh), Crystallography, X-Ray (mesh), Kinetics (mesh), Models, Molecular (mesh), Geobacillus stearothermophilus (mesh), DNA glycosylase, DNA repair, base excision repair, biochemistry, biology, catalysis, chemistry, protein evolution, protein structure, DNA Glycosylases (mesh), Geobacillus stearothermophilus (mesh), Crystallography, X-Ray (mesh), Adenine (mesh), Models, Molecular (mesh), Guanine (mesh), Kinetics (mesh), 0304 Medicinal and Biomolecular Chemistry (for), 0601 Biochemistry and Cell Biology (for), Organic Chemistry (science-metrix), 3101 Biochemistry and cell biology (for-2020), 3404 Medicinal and biomolecular chemistry (for-2020)

Περιγραφή αρχείου: application/pdf

Σύνδεσμος πρόσβασης: https://escholarship.org/uc/item/72q5z52b
https://escholarship.org/content/qt72q5z52b/qt72q5z52b.pdf

β-Fructosidases of Planctomycetes: Structure and Evolution

Συγγραφείς: Naumoff, D. G.^{Aff1, IDS002626172660179X_cor1}

Πηγή: Microbiology. 95(5):856-863

Key residues Tyr293, Val360, and Tyr399 regulate flavin stability in the plant cryptochrome from Chlamydomonas reinhardtii

Συγγραφείς: Wen, Bin^Aff1, Wan, Mengqi^Aff1, Liu, Hao^Aff1, Li, Xiaoran^Aff1, Guang, Xin^Aff1, Zhang, Jiaying^Aff1, Hu, Shuchang^Aff1, Wu, Rong^Aff1, Jiang, Shan^{Aff2, IDs43630026009987_cor1}, Lv, Jun^{Aff1, IDs43630026009987_cor2}

Πηγή: Photochemical & Photobiological Sciences. :1-15

Selection for Folding Stability Predicts Observed Covariation Between Protein Positions in the PDB

Συγγραφείς: Saebi, Fatemeh^Aff1, Minning, Jonas^Aff2, Bastolla, Ugo^{Aff1, IDs0023902610348x_cor1}

Πηγή: Journal of Molecular Evolution. :1-18

Evolutionary Transitions Drive Molecular Adaptation in Sculpin Rhodopsin

Συγγραφείς: Macpherson, Esmé S. B.^{Aff1, Aff2}, Chang, Belinda S. W.^{Aff2, Aff3}, Lovejoy, Nathan R.^{Aff1, Aff2, Aff3, IDs00239026103334_cor1}

Πηγή: Journal of Molecular Evolution. 94(4):711-725

Designing Peptide Fossils That Model the Evolution of the Bacterial Ferredoxin Fold

Συγγραφείς: Jagilinki, Bhanu P.^{aff1, aff2}, Campbell, Ian^aff3, Tyryshkin, Alexei M.^{aff1, aff2}, Mutter, Andrew C.^{aff1, aff2}, Siess, Jan^aff1, DiGiacomo, Juliana^aff1, Klein, Dylan^aff1, Poudel, Saroj^{aff1, aff2}, Falkowski, Paul G.^aff2, Silberg, Jonathan J.^aff3, Nanda, Vikas^aff1

Πηγή: JACS Au. 5(11):5414-5426

Διαθεσιμότητα: https://pubs.acs.org/doi/10.1021/jacsau.5c00863

Comprehensive analysis of small GTPases in Microsporidia reveals new extremes in eukaryotic cell biology

Συγγραφείς: Vargová, Romana^{Aff1, IDs1291502602639y_cor1}, Majnušová, Vladislava^Aff1, Eliáš, Marek^{Aff1, IDs1291502602639y_cor2}

Πηγή: BMC Biology. 24(1)

Structural evolution of iron coordination in proteins across earth’s oxygenation history

Συγγραφείς: Jelen, Benjamin I.^{Aff1, Aff2, IDs11084026097517_cor1}, Christensen, Beth^Aff1, Moore, Eli K.^Aff3

Πηγή: Discover Life. 56(1)

Evolution of intrinsically disordered regions in vertebrate galectins for phase separation

Συγγραφείς: Lin, Yu-Hao^{Aff1, Aff2}, Chen, Yu-Chen^Aff1, Sun, Yung-Chen^{Aff1, Aff2}, Huang, Jie-rong^{Aff1, Aff3, Aff4, IDs4431902600692w_cor1}

Πηγή: EMBO Reports. 27(5):1254-1269

Structural comparison of the influenza A H5N1 hemagglutinin protein models across the 2001–2024 strains reveals cross-species similarity in the 2024 avian, human, and mammalian variants

Συγγραφείς: Cueno, Marni E.^{Aff1, IDs42485026002052_cor1}, Imai, Kenichi^Aff1

Πηγή: Journal of Proteins and Proteomics: A Journal of the Proteomics Society, India (PSI). 17(1):1-11

Comparative Analysis of AlphaFold2 Models and Intrinsic Disorder Illuminates Structural Divergence as a Symptom of Functional Divergence Across the Calmodulin Superfamily

Συγγραφείς: Nakamura, Kyoko^Aff1, Siltberg-Liberles, Jessica^{Aff1, Aff2, IDs00239025102931_cor1}

Πηγή: Journal of Molecular Evolution. 94(1):149-163

Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (beta alpha)(8) Barrel Enzymes of Histidine and Tryptophan Biosynthesi

Συγγραφείς: Romero-Rivera, Adrian, Author, Corbella Morató, Marina, Author, Parracino, Antonietta, Author, Patrick, Wayne M., Author, Kamerlin, Shina C. Lynn, 1981-, Author

Συνεισφορές: Romero-Rivera, Adrian, Author, Corbella Morató, Marina, Author, Parracino, Antonietta, Author, Patrick, Wayne M., Author, Kamerlin, Shina C. Lynn, 1981-, Author

Πηγή: JACS Au. 2(4):943-960

Θεματικοί όροι: (beta alpha)(8)-barrel enzymes, protein evolution, catalytic promiscuity, computational enzymology, empirical valence bond, enhanced sampling

Περιγραφή αρχείου: electronic

Σύνδεσμος πρόσβασης: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-475110
https://doi.org/10.1021/jacsau.2c00063

Context dependent selection in molecular evolution

Συγγραφείς: Povolotskaya, Inna

Συνεισφορές: University/Department: Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut

Thesis Advisors: Kondrashov, Fyodor A.

Πηγή: TDX (Tesis Doctorals en Xarxa)

Θεματικοί όροι: Protein evolution, Selection, Epistasis, Fitness landscape, Evolución de las proteínas, Selección, Paisaje de fitness, Evolució molecular, Evolució de les proteïnes, Selecció

Περιγραφή αρχείου: application/pdf

Σύνδεσμος πρόσβασης: http://hdl.handle.net/10803/384000

Phylogenomics of Life Kingdom's Deubiquitinases

Συγγραφείς: Evpak, Alena, Evseev, Peter, Kudriaeva, Anna, Belogurov, Alexey

Πηγή: 2023 IEEE Ural-Siberian Conference on Computational Technologies in Cognitive Science, Genomics and Biomedicine (CSGB) Computational Technologies in Cognitive Science, Genomics and Biomedicine (CSGB), 2023 IEEE Ural-Siberian Conference on. :273-278 Sep, 2023

Relation: 2023 IEEE Ural-Siberian Conference on Computational Technologies in Cognitive Science, Genomics and Biomedicine (CSGB)

Mechanisms of evolutionary innovation in mammalian genes

Συγγραφείς: Toll i Riera, Macarena

Συνεισφορές: University/Department: Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut

Thesis Advisors: Albà Soler, Mar, Eyras Jiménez, Eduardo

Πηγή: TDX (Tesis Doctorals en Xarxa)

Θεματικοί όροι: Gens específics de primats, Tasses evolutives, Selecció positiva, Evolució, Determinants de l'evolució proteica, Mamífers, Mecanismes d'origen dels gens, Edat proteica, Primate-specific genes, Evolutionary rates, Positive selection, Evolution, Determinants for protein evolution, Mammals, Mechanisms of origin of the genes, Protein's age

Περιγραφή αρχείου: application/pdf

Σύνδεσμος πρόσβασης: http://hdl.handle.net/10803/92563

The Emergence of Novel Versus Known Three-Dimensional Structures from Random Sequences and Applications to De Novo Protein Design

Συγγραφείς: Yang, Rose

Θεματικοί όροι: Biophysics, Artificial intelligence, Molecular biology, Biochemistry, Machine learning, Protein design, Protein evolution, Structure prediction

Περιγραφή αρχείου: application/pdf

Σύνδεσμος πρόσβασης: https://escholarship.org/uc/item/37s6s4cw
https://escholarship.org/content/qt37s6s4cw/qt37s6s4cw.pdf

Phylogenomics using Compression Distances: Incorporating Rate Heterogeneity and Amino Acid Properties

Συγγραφείς: Braun, Edward L

Πηγή: Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. :1-6

Διαθεσιμότητα: http://dl.acm.org/doi/10.1145/3584371.3612996

Prevalent Fast Evolution of Genes Involved in Heterochromatin Functions

Συγγραφείς: Lin, Leila, Huang, Yuheng, McIntyre, Jennifer, Chang, Ching-Ho, Colmenares, Serafin, Lee, Yuh Chwen G

Πηγή: Molecular Biology and Evolution. 41(9)

Θεματικοί όροι: 31 Biological Sciences (for-2020), 3102 Bioinformatics and Computational Biology (for-2020), 3105 Genetics (for-2020), Genetics (rcdc), Human Genome (rcdc), Biotechnology (rcdc), 1.1 Normal biological development and functioning (hrcs-rac), 2.1 Biological and endogenous factors (hrcs-rac), Generic health relevance (hrcs-hc), Heterochromatin (mesh), Animals (mesh), Evolution, Molecular (mesh), DNA Transposable Elements (mesh), Drosophila (mesh), Selection, Genetic (mesh), Drosophila melanogaster (mesh), Gene Dosage (mesh), heterochromatin, protein evolution, transposable elements, repetitive sequences, arms race, positive selection, Heterochromatin (mesh), Animals (mesh), Drosophila (mesh), Drosophila melanogaster (mesh), DNA Transposable Elements (mesh), Evolution, Molecular (mesh), Gene Dosage (mesh), Selection, Genetic (mesh), arms race, heterochromatin, positive selection, protein evolution, repetitive sequences, transposable elements, Heterochromatin (mesh), Animals (mesh), Evolution, Molecular (mesh), DNA Transposable Elements (mesh), Drosophila (mesh), Selection, Genetic (mesh), Drosophila melanogaster (mesh), Gene Dosage (mesh), 0601 Biochemistry and Cell Biology (for), 0603 Evolutionary Biology (for), 0604 Genetics (for), Evolutionary Biology (science-metrix), 3101 Biochemistry and cell biology (for-2020), 3104 Evolutionary biology (for-2020), 3105 Genetics (for-2020)

Περιγραφή αρχείου: application/pdf

Σύνδεσμος πρόσβασης: https://escholarship.org/uc/item/1r39g2j9
https://escholarship.org/content/qt1r39g2j9/qt1r39g2j9.pdf

Lytic Enzymes Encoded in the Genome of Methyloraptor flagellatus S20T

Συγγραφείς: Naumoff, D. G.^{Aff1, IDS0026261725605871_cor1}, Saltykova, V. A.^Aff1, Dedysh, S. N.^Aff1

Πηγή: Microbiology. 94(Suppl 1):S143-S147