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Showing 1-20 from 46645 results
Title:
Accurate proteome-wide missense variant effect prediction with AlphaMissense.
Authors:
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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Source:
Science (New York, N.Y.) [Science] 2023 Sep 22; Vol. 381 (6664), pp. eadg7492. Date of Electronic Publication: 2023 Sep 22.
Publication Type:
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
Academic Journal
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Title:
Sequence Alignment-Based Prediction of Myosin 7A: Structural Implications and Protein Interactions.
Authors:
Yu CJ; Division of Chemistry & Biochemistry, Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
Park YH; Division of Chemistry & Biochemistry, Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
Ryu B; Research Solution Center, Institute for Basic Science, Daejeon 34126, Republic of Korea.
Jung HS; Division of Chemistry & Biochemistry, Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
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Source:
International journal of molecular sciences [Int J Mol Sci] 2024 Mar 16; Vol. 25 (6). Date of Electronic Publication: 2024 Mar 16.
Publication Type:
Journal Article
MeSH Terms:
Actins*/metabolism
Myosins*/metabolism
Sequence Alignment ; Protein Structure, Tertiary ; Protein Binding ; Protein Isoforms/metabolism ; Adenosine Triphosphate/metabolism
Academic Journal
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Title:
Unveiling hidden structural patterns in the SARS-CoV-2 genome: Computational insights and comparative analysis.
Authors:
Ziesel A; Department of Biomedical Engineering, University of Alberta, Edmonton, Alberta, Canada.
Jabbari H; Department of Biomedical Engineering, University of Alberta, Edmonton, Alberta, Canada.
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Source:
PloS one [PLoS One] 2024 Apr 04; Vol. 19 (4), pp. e0298164. Date of Electronic Publication: 2024 Apr 04 (Print Publication: 2024).
Publication Type:
Journal Article
MeSH Terms:
SARS-CoV-2*/genetics
COVID-19*/genetics
Humans ; Sequence Alignment ; Genome, Viral/genetics ; RNA, Viral/genetics ; RNA, Viral/chemistry
Academic Journal
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Title:
TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments.
Authors:
Zhai Y; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.; Quzhou People's Hospital, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China.; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China.
Chao J; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China.
Wang Y; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China.
Zhang P; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China.
Tang F; Quzhou People's Hospital, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China.; Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
Zou Q; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China.
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Source:
PLoS computational biology [PLoS Comput Biol] 2024 Apr 01; Vol. 20 (4), pp. e1011988. Date of Electronic Publication: 2024 Apr 01 (Print Publication: 2024).
Publication Type:
Journal Article
MeSH Terms:
Algorithms*
Nucleic Acids*
Sequence Alignment ; Coffee ; Software
Academic Journal
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Title:
Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration.
Authors:
Fang T; Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
Szklarczyk D; Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
Hachilif R; Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
von Mering C; Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland. .; SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland. .
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Source:
Scientific reports [Sci Rep] 2024 Mar 12; Vol. 14 (1), pp. 6009. Date of Electronic Publication: 2024 Mar 12.
Publication Type:
Journal Article
MeSH Terms:
Algorithms*
Proteins*/genetics
Sequence Alignment ; Biological Evolution ; Phylogeny ; Computational Biology/methods
Academic Journal
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Title:
CNCA aligns small annotated genomes.
Authors:
Lorenzi JN; Université Paris Cité, Paris, France. .; CNRS, Institut Jacques Monod, 75013, Paris, France. .; SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, 75006, Paris, France. .
Graner F; Université Paris Cité, Paris, France.; CNRS, Matière Et Systèmes Complexes, 75013, Paris, France.
Courtier-Orgogozo V; Université Paris Cité, Paris, France.; CNRS, Institut Jacques Monod, 75013, Paris, France.
Achaz G; SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, 75006, Paris, France.
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Source:
BMC bioinformatics [BMC Bioinformatics] 2024 Feb 29; Vol. 25 (1), pp. 89. Date of Electronic Publication: 2024 Feb 29.
Publication Type:
Journal Article
MeSH Terms:
Genome*
Proteins*
Sequence Alignment ; Amino Acid Sequence ; Nucleotides
Academic Journal
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Title:
KINtaro: protein kinase-like database.
Authors:
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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Source:
BMC research notes [BMC Res Notes] 2024 Feb 16; Vol. 17 (1), pp. 50. Date of Electronic Publication: 2024 Feb 16.
Publication Type:
Journal Article
MeSH Terms:
Protein Kinases*/genetics
Proteins*
Humans ; Phosphorylation ; Amino Acid Sequence ; Sequence Alignment ; Databases, Protein
Academic Journal
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Title:
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format.
Authors:
Bessa-Silva A; Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil. .
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Source:
BMC bioinformatics [BMC Bioinformatics] 2024 Feb 15; Vol. 25 (1), pp. 73. Date of Electronic Publication: 2024 Feb 15.
Publication Type:
Journal Article
MeSH Terms:
Software*
User-Computer Interface*
Sequence Alignment
Academic Journal
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Title:
De novo prediction of RNA 3D structures with deep generative models.
Authors:
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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Source:
PloS one [PLoS One] 2024 Feb 15; Vol. 19 (2), pp. e0297105. Date of Electronic Publication: 2024 Feb 15 (Print Publication: 2024).
Publication Type:
Journal Article
MeSH Terms:
RNA*/chemistry
Retrospective Studies ; Sequence Alignment ; Base Sequence
Academic Journal
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Title:
Cloning and Characterization of Chitin Deacetylase from Euphausia superba .
Authors:
Wang X; College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China.
Tan J; College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China.
Zou H; College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China.
Wang F; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China.; Key Laboratory of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China.
Xu J; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China.; Key Laboratory of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China.
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Source:
International journal of molecular sciences [Int J Mol Sci] 2024 Feb 08; Vol. 25 (4). Date of Electronic Publication: 2024 Feb 08.
Publication Type:
Journal Article
MeSH Terms:
Euphausiacea*
Animals ; Cloning, Molecular ; Sequence Alignment ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Amidohydrolases/metabolism ; Chitin
Academic Journal
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Title:
Leveraging genomic redundancy to improve inference and alignment of orthologous proteins.
Authors:
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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Source:
G3 (Bethesda, Md.) [G3 (Bethesda)] 2023 Dec 06; Vol. 13 (12).
Publication Type:
Journal Article
MeSH Terms:
Genomics*
Algorithms*
Phylogeny ; Sequence Alignment ; Computational Biology/methods ; Proteins/genetics
Academic Journal
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Title:
The evolutionary loss of the Eh1 motif in FoxE1 in the lineage of placental mammals.
Authors:
Sharma M; Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, United States of America.
Larow VM; Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, United States of America.
Dobychina N; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.
Kessler DS; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
Krasilnikova MM; Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, United States of America.
Yaklichkin S; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.
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Source:
PloS one [PLoS One] 2023 Dec 27; Vol. 18 (12), pp. e0296176. Date of Electronic Publication: 2023 Dec 27 (Print Publication: 2023).
Publication Type:
Journal Article
MeSH Terms:
Eutheria*/metabolism
Placenta*/metabolism
Pregnancy ; Animals ; Female ; Thyroid Gland/metabolism ; Forkhead Transcription Factors/genetics ; Forkhead Transcription Factors/metabolism ; Sequence Alignment
Academic Journal
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Title:
Portable BLAST-like algorithm library and its implementations for command line, Python, and R.
Authors:
Schmid S; hakuna AG, Zürich, Switzerland.
Jeevannavar A; Department of Biology, University of Turku, Turku, Finland.
Julian TR; Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
Tamminen M; Department of Biology, University of Turku, Turku, Finland.
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Source:
PloS one [PLoS One] 2023 Nov 30; Vol. 18 (11), pp. e0289693. Date of Electronic Publication: 2023 Nov 30 (Print Publication: 2023).
Publication Type:
Journal Article
MeSH Terms:
Software*
Algorithms*
Phylogeny ; Sequence Alignment ; Programming Languages ; Computational Biology
Academic Journal
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Title:
Exploring complexity of class-A Beta-lactamase family using physiochemical-based multiplex networks.
Authors:
Bhadola P; Centre for Theoretical Physics & Natural Philosophy, Mahidol University, Nakhonsawan Campus, Phayuha Khiri, NakhonSawan, 60130, Thailand. .
Deo N; Department of Physics and Astrophysics, University of Delhi, Delhi, 110007, India. .
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Source:
Scientific reports [Sci Rep] 2023 Nov 23; Vol. 13 (1), pp. 20626. Date of Electronic Publication: 2023 Nov 23.
Publication Type:
Journal Article
MeSH Terms:
beta-Lactamases*/metabolism
Proteins*/chemistry
Biological Evolution ; Sequence Alignment ; Amino Acids ; beta-Lactamase Inhibitors ; Anti-Bacterial Agents
Academic Journal
Full Text  Link opens in a new window Full TextDetails
Title:
A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins.
Authors:
Cao W; Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Wu LY; Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Xia XY; Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Chen X; Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Wang ZX; Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .
Pan XM; Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .
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Source:
Scientific reports [Sci Rep] 2023 Nov 20; Vol. 13 (1), pp. 20304. Date of Electronic Publication: 2023 Nov 20.
Publication Type:
Journal Article
MeSH Terms:
Evolution, Molecular*
Biological Evolution*
Phylogeny ; Sequence Alignment ; Proteins/genetics ; Proteins/chemistry ; Algorithms
Academic Journal
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Title:
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches.
Authors:
Titarenko V; School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, UK. .
Titarenko S; School of Mathematics, University of Leeds, Woodhouse, Leeds, LS2 9JT, UK.
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Source:
BMC bioinformatics [BMC Bioinformatics] 2023 Oct 24; Vol. 24 (1), pp. 396. Date of Electronic Publication: 2023 Oct 24.
Publication Type:
Journal Article
MeSH Terms:
Algorithms*
Data Compression*
Sequence Alignment ; Sequence Analysis/methods ; Sequence Analysis, DNA/methods ; Software
Academic Journal
Full Text  Link opens in a new window Full TextDetails
Showing 1-20 from 46645 results

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