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Wyszukujesz frazę ""Sequence Alignment"" wg kryterium: Temat


Tytuł:
Gauging Dynamics-driven Allostery Using a New Computational Tool: A CAP Case Study.
Autorzy:
Kornev AP; Departmen of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA. Electronic address: .
Weng JH; Departmen of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA.
Maillard RA; Department of Chemistry, Georgetown University, Washington, DC 20007, USA.
Taylor SS; Departmen of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
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Źródło:
Journal of molecular biology [J Mol Biol] 2024 Jan 15; Vol. 436 (2), pp. 168395. Date of Electronic Publication: 2023 Dec 13.
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms:
Allosteric Regulation*
Cyclic AMP Receptor Protein*/chemistry
Sequence Alignment*/methods
Entropy ; Molecular Dynamics Simulation ; Protein Binding ; Reproducibility of Results
Czasopismo naukowe
Tytuł:
Multiple sequence alignment-based RNA language model and its application to structural inference.
Autorzy:
Zhang Y; School of Electronic and Computer Engineering, Peking University, Shenzhen 518055, China.; AI for Science (AI4S)-Preferred Program, Peking University Shenzhen Graduate School, Shenzen 518055, China.
Lang M; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China.
Jiang J; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China.
Gao Z; Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China.; Peng Cheng Laboratory, Shenzhen 518066, China.
Xu F; Peng Cheng Laboratory, Shenzhen 518066, China.
Litfin T; Institute for Glycomics, Griffith University, Parklands Dr, Southport, QLD 4215, Australia.
Chen K; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China.
Singh J; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China.
Huang X; Peng Cheng Laboratory, Shenzhen 518066, China.
Song G; Peng Cheng Laboratory, Shenzhen 518066, China.
Tian Y; Peng Cheng Laboratory, Shenzhen 518066, China.
Zhan J; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China.
Chen J; School of Electronic and Computer Engineering, Peking University, Shenzhen 518055, China.; Peng Cheng Laboratory, Shenzhen 518066, China.
Zhou Y; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China.; Institute for Glycomics, Griffith University, Parklands Dr, Southport, QLD 4215, Australia.
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Źródło:
Nucleic acids research [Nucleic Acids Res] 2024 Jan 11; Vol. 52 (1), pp. e3.
Typ publikacji:
Journal Article
MeSH Terms:
RNA*/chemistry
Sequence Alignment*
Machine Learning*
DNA/chemistry ; Proteins ; Solvents
Czasopismo naukowe
Tytuł:
Predicting multiple conformations via sequence clustering and AlphaFold2.
Autorzy:
Wayment-Steele HK; Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.
Ojoawo A; Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.
Otten R; Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.; Treeline Biosciences, Watertown, MA, USA.
Apitz JM; Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.
Pitsawong W; Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.; Biomolecular Discovery, Relay Therapeutics, Cambridge, MA, USA.
Hömberger M; Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.; Treeline Biosciences, Watertown, MA, USA.
Ovchinnikov S; Center for Systems Biology, Harvard University, Cambridge, MA, USA.
Colwell L; Google Research, Cambridge, MA, USA.; Cambridge University, Cambridge, UK.
Kern D; Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA. .
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Źródło:
Nature [Nature] 2024 Jan; Vol. 625 (7996), pp. 832-839. Date of Electronic Publication: 2023 Nov 13.
Typ publikacji:
Journal Article
MeSH Terms:
Cluster Analysis*
Protein Conformation*
Proteins*/chemistry
Proteins*/genetics
Proteins*/metabolism
Sequence Alignment*
Machine Learning*
Protein Folding*
Mutation ; Rhodobacter sphaeroides ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism
Czasopismo naukowe
Tytuł:
Accurate proteome-wide missense variant effect prediction with AlphaMissense.
Autorzy:
Cheng J; Google DeepMind, London, UK.
Novati G; Google DeepMind, London, UK.
Pan J; Google DeepMind, London, UK.
Bycroft C; Google DeepMind, London, UK.
Žemgulytė A; Google DeepMind, London, UK.
Applebaum T; Google DeepMind, London, UK.
Pritzel A; Google DeepMind, London, UK.
Wong LH; Google DeepMind, London, UK.
Zielinski M; Google DeepMind, London, UK.
Sargeant T; Google DeepMind, London, UK.
Schneider RG; Google DeepMind, London, UK.
Senior AW; Google DeepMind, London, UK.
Jumper J; Google DeepMind, London, UK.
Hassabis D; Google DeepMind, London, UK.
Kohli P; Google DeepMind, London, UK.
Avsec Ž; Google DeepMind, London, UK.
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Źródło:
Science (New York, N.Y.) [Science] 2023 Sep 22; Vol. 381 (6664), pp. eadg7492. Date of Electronic Publication: 2023 Sep 22.
Typ publikacji:
Journal Article
MeSH Terms:
Amino Acid Substitution*/genetics
Disease*/genetics
Mutation, Missense*
Proteome*/genetics
Sequence Alignment*/methods
Humans ; Benchmarking ; Conserved Sequence ; Databases, Genetic ; Genome, Human ; Protein Conformation ; Machine Learning
Czasopismo naukowe
Tytuł:
DCAlign v1.0: aligning biological sequences using co-evolution models and informed priors.
Autorzy:
Muntoni AP; Italian Institute for Genomic Medicine, IRCCS Candiolo, I-10060 Candiolo (TO), Italy.; Politecnico di Torino, I-10129 Torino, Italy.
Pagnani A; Italian Institute for Genomic Medicine, IRCCS Candiolo, I-10060 Candiolo (TO), Italy.; Politecnico di Torino, I-10129 Torino, Italy.; INFN, Sezione di Torino, Torino, Via Pietro Giuria 1, I-10125 Torino, Italy.
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Źródło:
Bioinformatics (Oxford, England) [Bioinformatics] 2023 Sep 02; Vol. 39 (9).
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Sequence Alignment*
Computational Biology
Czasopismo naukowe
Tytuł:
CovET: A covariation-evolutionary trace method that identifies protein structure-function modules.
Autorzy:
Konecki DM; Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, Texas, USA.
Hamrick S; Chemical, Physical, and Structural Biology Graduate Program, Baylor College of Medicine, Houston, Texas, USA.
Wang C; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
Agosto MA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.
Wensel TG; Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA; Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, Texas, USA.
Lichtarge O; Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA; Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, Texas, USA; Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas, USA. Electronic address: .
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Źródło:
The Journal of biological chemistry [J Biol Chem] 2023 Jul; Vol. 299 (7), pp. 104896. Date of Electronic Publication: 2023 Jun 07.
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms:
Evolution, Molecular*
Sequence Alignment*/methods
Binding Sites/genetics ; Phylogeny ; Receptors, G-Protein-Coupled/genetics
Czasopismo naukowe
Tytuł:
CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching.
Autorzy:
Chen X; Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.
Zhang S; Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.
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Źródło:
Nucleic acids research [Nucleic Acids Res] 2023 May 22; Vol. 51 (9), pp. e53.
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms:
Nucleic Acid Conformation*
RNA*/genetics
RNA*/chemistry
Sequence Alignment*/methods
Sequence Analysis, RNA*/methods
Software*
Algorithms ; Base Pairing
Czasopismo naukowe
Tytuł:
FAS: assessing the similarity between proteins using multi-layered feature architectures.
Autorzy:
Dosch J; Applied Bioinformatics Group, Goethe University Frankfurt, Faculty of Biosciences, Institute of Cell Biology and Neuroscience, Frankfurt, 60438, Germany.
Bergmann H; Applied Bioinformatics Group, Goethe University Frankfurt, Faculty of Biosciences, Institute of Cell Biology and Neuroscience, Frankfurt, 60438, Germany.
Tran V; Applied Bioinformatics Group, Goethe University Frankfurt, Faculty of Biosciences, Institute of Cell Biology and Neuroscience, Frankfurt, 60438, Germany.
Ebersberger I; Applied Bioinformatics Group, Goethe University Frankfurt, Faculty of Biosciences, Institute of Cell Biology and Neuroscience, Frankfurt, 60438, Germany.; Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt, 60325, Germany.; LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt, 60325, Germany.
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Źródło:
Bioinformatics (Oxford, England) [Bioinformatics] 2023 May 04; Vol. 39 (5).
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Amino Acid Sequence*
Proteins*/chemistry
Software*
Sequence Alignment*/methods
Humans ; Computational Biology/methods ; Saccharomyces cerevisiae Proteins/chemistry
Czasopismo naukowe
Tytuł:
VF-Pred: Predicting virulence factor using sequence alignment percentage and ensemble learning models.
Autorzy:
Singh S; NUS-ISS, National University of Singapore, 119615, Singapore.
Le NQK; Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan; AIBioMed Research Group, Taipei Medical University, Taipei, 110, Taiwan; Translational Imaging Research Center, Taipei Medical University Hospital, Taipei, 110, Taiwan. Electronic address: .
Wang C; NUS-ISS, National University of Singapore, 119615, Singapore.
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Źródło:
Computers in biology and medicine [Comput Biol Med] 2024 Jan; Vol. 168, pp. 107662. Date of Electronic Publication: 2023 Nov 03.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Virulence Factors*/genetics
Communicable Diseases*
Humans ; Sequence Alignment ; Algorithms ; Machine Learning
Czasopismo naukowe
Tytuł:
Leveraging genomic redundancy to improve inference and alignment of orthologous proteins.
Autorzy:
Singleton M; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA.
Eisen M; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA.; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
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Źródło:
G3 (Bethesda, Md.) [G3 (Bethesda)] 2023 Dec 06; Vol. 13 (12).
Typ publikacji:
Journal Article
MeSH Terms:
Genomics*
Algorithms*
Phylogeny ; Sequence Alignment ; Computational Biology/methods ; Proteins/genetics
Czasopismo naukowe
Tytuł:
Improved protein structure prediction with trRosettaX2, AlphaFold2, and optimized MSAs in CASP15.
Autorzy:
Peng Z; MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China.
Wang W; School of Mathematical Sciences, Nankai University, Tianjin, China.
Wei H; School of Mathematical Sciences, Nankai University, Tianjin, China.
Li X; MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China.
Yang J; MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China.
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Źródło:
Proteins [Proteins] 2023 Dec; Vol. 91 (12), pp. 1704-1711. Date of Electronic Publication: 2023 Aug 10.
Typ publikacji:
Journal Article
MeSH Terms:
Furylfuramide*
Algorithms*
Sequence Alignment ; Databases, Nucleic Acid
Czasopismo naukowe
Tytuł:
KINtaro: protein kinase-like database.
Autorzy:
Baranowski B; Laboratory of Plant Pathogenesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
Krysińska M; Department of Biochemistry and Microbiology, Warsaw University of Life Sciences (SGGW), Warsaw, Poland.
Gradowski M; Department of Biochemistry and Microbiology, Warsaw University of Life Sciences (SGGW), Warsaw, Poland. marcin_.
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Źródło:
BMC research notes [BMC Res Notes] 2024 Feb 16; Vol. 17 (1), pp. 50. Date of Electronic Publication: 2024 Feb 16.
Typ publikacji:
Journal Article
MeSH Terms:
Protein Kinases*/genetics
Proteins*
Humans ; Phosphorylation ; Amino Acid Sequence ; Sequence Alignment ; Databases, Protein
Czasopismo naukowe
Tytuł:
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format.
Autorzy:
Bessa-Silva A; Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2024 Feb 15; Vol. 25 (1), pp. 73. Date of Electronic Publication: 2024 Feb 15.
Typ publikacji:
Journal Article
MeSH Terms:
Software*
User-Computer Interface*
Sequence Alignment
Czasopismo naukowe
Tytuł:
De novo prediction of RNA 3D structures with deep generative models.
Autorzy:
Ramakers J; Department of Computer Science, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
Blum CF; Department of Computer Science, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
König S; Department of Computer Science, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
Harmeling S; Department of Computer Science, Technical University Dortmund, Dortmund, Germany.
Kollmann M; Department of Computer Science, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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Źródło:
PloS one [PLoS One] 2024 Feb 15; Vol. 19 (2), pp. e0297105. Date of Electronic Publication: 2024 Feb 15 (Print Publication: 2024).
Typ publikacji:
Journal Article
MeSH Terms:
RNA*/chemistry
Retrospective Studies ; Sequence Alignment ; Base Sequence
Czasopismo naukowe
Tytuł:
TM-search: An Efficient and Effective Tool for Protein Structure Database Search.
Autorzy:
Liu Z; School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China.; Computer Department, Jingdezhen Ceramic University, Jingdezhen 333403, China.
Zhang C; Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw, Ann Arbor, Michigan 48109-2218, United States.
Zhang Q; Computer Department, Jingdezhen Ceramic University, Jingdezhen 333403, China.
Zhang Y; Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw, Ann Arbor, Michigan 48109-2218, United States.
Yu DJ; School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China.
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Źródło:
Journal of chemical information and modeling [J Chem Inf Model] 2024 Feb 12; Vol. 64 (3), pp. 1043-1049. Date of Electronic Publication: 2024 Jan 25.
Typ publikacji:
Journal Article
MeSH Terms:
Algorithms*
Proteins*/chemistry
Databases, Protein ; Sequence Alignment ; Benchmarking ; Software
Czasopismo naukowe
Tytuł:
Statistical framework to determine indel-length distribution.
Autorzy:
Wygoda E; The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Loewenthal G; The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Moshe A; The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Alburquerque M; The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Mayrose I; School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Pupko T; The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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Źródło:
Bioinformatics (Oxford, England) [Bioinformatics] 2024 Feb 01; Vol. 40 (2).
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Algorithms*
Bayes Theorem ; Sequence Alignment ; INDEL Mutation ; Evolution, Molecular
Czasopismo naukowe
Tytuł:
The Site/Group Extended Data Format and Tools.
Autorzy:
Dutheil JY; Research Group 'Molecular Systems Evolution,' Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.
Hamidi D; Research Group 'Molecular Systems Evolution,' Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.
Pajot B; Research Group 'Molecular Systems Evolution,' Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.
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Źródło:
Genome biology and evolution [Genome Biol Evol] 2024 Feb 01; Vol. 16 (2).
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Evolution, Molecular*
Sequence Alignment ; Sequence Analysis
Czasopismo naukowe
Tytuł:
DsRNA sequencing revealed a previously missed terminal sequence of a +ssRNA virus that infects dinoflagellate Heterocapsa circularisquama.
Autorzy:
Takahashi M; Kochi Medical School, Kochi University, Nankoku, Kochi, 783-8505, Japan.
Masuda Y; Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, 783-8502, Japan.
Chiba Y; Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
Urayama SI; Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
Nagasaki K; Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, 783-8502, Japan. .
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Źródło:
Virus genes [Virus Genes] 2024 Feb; Vol. 60 (1), pp. 97-99. Date of Electronic Publication: 2024 Jan 10.
Typ publikacji:
Journal Article
MeSH Terms:
Viruses*/genetics
RNA Viruses*/genetics
Dinoflagellida*/genetics
RNA, Double-Stranded/genetics ; Sequence Alignment ; RNA, Viral/genetics
Czasopismo naukowe
Tytuł:
Singapore grouper iridovirus VP20 interacts with grouper TBK1 and IRF3 to attenuate the interferon immune response.
Autorzy:
Liu S; College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
Wang Y; College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
Wang W; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511464, China.
Zhi L; College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
Zhao Y; College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
Qin Q; College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511464, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, 519082, China.
Huang Y; College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511464, China. Electronic address: .
Huang X; College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511464, China. Electronic address: .
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Źródło:
Fish & shellfish immunology [Fish Shellfish Immunol] 2024 Feb; Vol. 145, pp. 109349. Date of Electronic Publication: 2024 Jan 04.
Typ publikacji:
Journal Article
MeSH Terms:
Ranavirus*/physiology
Bass*
Iridovirus*
Fish Diseases*
DNA Virus Infections*
Animals ; Interferons ; Immunity, Innate/genetics ; Singapore ; Amino Acid Sequence ; Fish Proteins/genetics ; Sequence Alignment
Czasopismo naukowe

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