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Wyświetlanie 1-15 z 15
Tytuł :
3D genomics across the tree of life reveals condensin II as a determinant of architecture type.
Autorzy :
Hoencamp C; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
Dudchenko O; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
Elbatsh AMO; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
Brahmachari S; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
Raaijmakers JA; Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
van Schaik T; Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
Sedeño Cacciatore Á; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
Contessoto VG; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto - SP, 15054-000, Brazil.
van Heesbeen RGHP; Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
van den Broek B; BioImaging Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
Mhaskar AN; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
Teunissen H; Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
St Hilaire BG; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Weisz D; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Omer AD; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Pham M; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Colaric Z; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Yang Z; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China.
Rao SSP; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Mitra N; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Lui C; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Yao W; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Khan R; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Moroz LL; Whitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA.
Kohn A; Whitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA.
St Leger J; Department of Biosciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA.
Mena A; SeaWorld San Diego, San Diego, CA 92109, USA.
Holcroft K; Moody Gardens, Galveston, TX 77554, USA.
Gambetta MC; Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
Lim F; Department of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
Farley E; Department of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
Stein N; Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), 06466 Seeland, Germany.; Center of Integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University Göttingen, 37075 Göttingen, Germany.; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.
Haddad A; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Chauss D; National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Mutlu AS; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Wang MC; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA.; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
Young ND; Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia.
Hildebrandt E; Avian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA.
Cheng HH; Avian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA.
Knight CJ; Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA.
Burnham TLU; Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA 95616, USA.; Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA.
Hovel KA; Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA.
Beel AJ; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Mattei PJ; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Kornberg RD; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Warren WC; Department of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
Cary G; The Jackson Laboratory, Bar Harbor, ME 04609, USA.
Gómez-Skarmeta JL; Centro Andaluz de Biología del Desarrollo CSIC, Universidad Pablo de Olavide, 41013 Sevilla, Spain.
Hinman V; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Lindblad-Toh K; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.
Di Palma F; Department of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
Maeshima K; Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.; Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan.
Multani AS; Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Pathak S; Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Nel-Themaat L; Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Behringer RR; Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Kaur P; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.
Medema RH; Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
van Steensel B; Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
de Wit E; Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
Onuchic JN; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, TX 77005, USA.
Di Pierro M; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; Department of Physics, Northeastern University, Boston, MA 02115, USA.
Lieberman Aiden E; The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA. .; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China.; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Rowland BD; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands. .
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Źródło :
Science (New York, N.Y.) [Science] 2021 May 28; Vol. 372 (6545), pp. 984-989.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Biological Evolution*
Genome*
Adenosine Triphosphatases/*genetics
Adenosine Triphosphatases/*physiology
Chromosomes/*ultrastructure
DNA-Binding Proteins/*genetics
DNA-Binding Proteins/*physiology
Eukaryota/*genetics
Multiprotein Complexes/*genetics
Multiprotein Complexes/*physiology
Adenosine Triphosphatases/chemistry ; Algorithms ; Animals ; Cell Nucleolus/ultrastructure ; Cell Nucleus/ultrastructure ; Centromere/ultrastructure ; Chromosomes/chemistry ; Chromosomes, Human/chemistry ; Chromosomes, Human/ultrastructure ; DNA-Binding Proteins/chemistry ; Genome, Human ; Genomics ; Heterochromatin/ultrastructure ; Humans ; Interphase ; Mitosis ; Models, Biological ; Multiprotein Complexes/chemistry ; Telomere/ultrastructure
Czasopismo naukowe
Tytuł :
Improving the Thermostability of Xylanase A from Bacillus subtilis by Combining Bioinformatics and Electrostatic Interactions Optimization.
Autorzy :
Ngo K; Department of Physics, University of Houston, Houston, Texas 77004, United States.
Bruno da Silva F; Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas UNESP - Univ. Estadual Paulista, São José do Rio Preto, SP, Brazil.
Leite VBP; Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas UNESP - Univ. Estadual Paulista, São José do Rio Preto, SP, Brazil.
Contessoto VG; Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas UNESP - Univ. Estadual Paulista, São José do Rio Preto, SP, Brazil.
Onuchic JN
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Źródło :
The journal of physical chemistry. B [J Phys Chem B] 2021 May 06; Vol. 125 (17), pp. 4359-4367. Date of Electronic Publication: 2021 Apr 22.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
Czasopismo naukowe
Tytuł :
A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes.
Autorzy :
Oliveira Junior AB; Center for Theoretical Biological Physics, Rice University, Houston, TX, USA; ICTP South American Institute for Fundamental Research, Instituto de Física Teórica, UNESP - 01140-070, São Paulo, SP, Brazil. Electronic address: .
Contessoto VG; Center for Theoretical Biological Physics, Rice University, Houston, TX, USA; Instituto de Biociências, Letras e Ciências Exatas, UNESP - Univ. Estadual Paulista, Departamento de Física, São José do Rio Preto, SP, Brazil. Electronic address: vinicius.contessoto@rice.edu.
Mello MF; Center for Theoretical Biological Physics, Rice University, Houston, TX, USA; Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil.
Onuchic JN; Center for Theoretical Biological Physics, Rice University, Houston, TX, USA; ICTP South American Institute for Fundamental Research, Instituto de Física Teórica, UNESP - 01140-070, São Paulo, SP, Brazil. Electronic address: .
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Źródło :
Journal of molecular biology [J Mol Biol] 2021 Mar 19; Vol. 433 (6), pp. 166700. Date of Electronic Publication: 2020 Nov 06.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Molecular Dynamics Simulation*
Software*
Chromatin/*chemistry
Chromosomes, Human, Pair 1/*chemistry
Chromosomes, Human, Pair 2/*chemistry
Chromosomes, Human, Pair 3/*chemistry
Chromosomes, Human, Pair 4/*chemistry
Animals ; Cell Line, Tumor ; Chromatin/metabolism ; Chromatin/ultrastructure ; Chromosomes, Human, Pair 1/metabolism ; Chromosomes, Human, Pair 1/ultrastructure ; Chromosomes, Human, Pair 2/metabolism ; Chromosomes, Human, Pair 2/ultrastructure ; Chromosomes, Human, Pair 3/metabolism ; Chromosomes, Human, Pair 3/ultrastructure ; Chromosomes, Human, Pair 4/metabolism ; Chromosomes, Human, Pair 4/ultrastructure ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Humans ; Lymphocytes/cytology ; Lymphocytes/metabolism ; Saccharum/genetics ; Saccharum/metabolism ; Thermodynamics ; Triticum/genetics ; Triticum/metabolism
Czasopismo naukowe
Tytuł :
Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain.
Autorzy :
Staquicini DI
Tang FHF
Markosian C
Yao VJ
Staquicini FI
Dodero-Rojas E
Contessoto VG
Davis D
O'Brien P
Habib N
Smith TL
Bruiners N
Sidman RL
Gennaro ML
Lattime EC
Libutti SK
Whitford PC
Burley SK
Onuchic JN
Arap W
Pasqualini R
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Źródło :
BioRxiv : the preprint server for biology [bioRxiv] 2021 Mar 16. Date of Electronic Publication: 2021 Mar 16.
Typ publikacji :
Preprint
Tytuł :
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome.
Autorzy :
Contessoto VG; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; Brazilian Biorenewables National Laboratory-LNBR, Brazilian Center for Research in Energy and Materials-CNPEM, Campinas, SP 13083-100, Brazil.; Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil.
Cheng RR; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
Hajitaheri A; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; Department of Computer Science, University of Houston, Houston, TX 77204, USA.
Dodero-Rojas E; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; Theoretical and Computational Physics Laboratory, University of Costa Rica, San José 5 11501, Costa Rica.
Mello MF; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil.
Lieberman-Aiden E; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Wolynes PG; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; Department of Physics & Astronomy, Rice University, Houston, TX 77005, USA.; Department of Chemistry, Rice University, Houston, TX 77005, USA.; Department of Biosciences, Rice University, Houston, TX 77005, USA.
Di Pierro M; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; Department of Physics, Northeastern University, Boston, MA 02115, USA.
Onuchic JN; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.; Department of Physics & Astronomy, Rice University, Houston, TX 77005, USA.; Department of Chemistry, Rice University, Houston, TX 77005, USA.; Department of Biosciences, Rice University, Houston, TX 77005, USA.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2021 Jan 08; Vol. 49 (D1), pp. D172-D182.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Databases, Genetic*
Epigenesis, Genetic*
Genome, Human*
Chromatin/*ultrastructure
Computational Biology/*methods
A549 Cells ; Chromatin/metabolism ; Humans ; In Situ Hybridization, Fluorescence ; Internet ; Molecular Conformation ; Molecular Sequence Annotation ; Software
Czasopismo naukowe
Tytuł :
Exploring chromosomal structural heterogeneity across multiple cell lines.
Autorzy :
Cheng RR; Center for Theoretical Biological Physics, Rice University, Houston, United States.
Contessoto VG; Center for Theoretical Biological Physics, Rice University, Houston, United States.; Brazilian Biorenewables National Laboratory - LNBR, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil.
Lieberman Aiden E; Center for Theoretical Biological Physics, Rice University, Houston, United States.; Center for Genome Architecture, Baylor College of Medicine, Houston, United States.
Wolynes PG; Center for Theoretical Biological Physics, Rice University, Houston, United States.; Department of Chemistry, Rice University, Houston, United States.; Department of Physics & Astronomy, Rice University, Houston, United States.; Department of Biosciences, Rice University, Houston, United States.
Di Pierro M; Center for Theoretical Biological Physics, Rice University, Houston, United States.; Department of Physics, Northeastern University, Boston, United States.
Onuchic JN; Center for Theoretical Biological Physics, Rice University, Houston, United States.; Department of Chemistry, Rice University, Houston, United States.; Department of Physics & Astronomy, Rice University, Houston, United States.; Department of Biosciences, Rice University, Houston, United States.
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Źródło :
ELife [Elife] 2020 Oct 13; Vol. 9. Date of Electronic Publication: 2020 Oct 13.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Chromosomes, Human/*ultrastructure
Cell Line ; Cell Line, Tumor ; Chromatin/metabolism ; Chromatin/ultrastructure ; Computer Simulation ; Epigenesis, Genetic ; Genetic Loci ; Humans ; Imaging, Three-Dimensional
Czasopismo naukowe
Tytuł :
AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes.
Autorzy :
Jin S; Department of Biosciences, Rice University, 6100 Main St, Houston, TX 77005, USA.; Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.
Contessoto VG; Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.
Chen M; Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.
Schafer NP; Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.
Lu W; Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.; Department of Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.
Chen X; Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.; Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA.
Bueno C; Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.
Hajitaheri A; Department of Computer Science, University of Houston, 4800 Calhoun Rd, Houston, TX 77004, USA.
Sirovetz BJ; Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.
Davtyan A; Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.
Papoian GA; Department of Chemistry, University of Maryland, College Park, MD 20742, USA.
Tsai MY; Department of Chemistry, Tamkang University, 151 Yingzhuan Road, New Taipei City 25137, Taiwan.
Wolynes PG; Department of Biosciences, Rice University, 6100 Main St, Houston, TX 77005, USA.; Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.; Department of Physics, Rice University, 6100 Main St, Houston, TX 77005, USA.; Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Jul 02; Vol. 48 (W1), pp. W25-W30.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Protein Structure, Tertiary*
Software*
Algorithms ; Evolution, Molecular ; Protein Folding ; Sequence Analysis, Protein ; Structural Homology, Protein
Czasopismo naukowe
Tytuł :
Rational Design of Chymotrypsin Inhibitor 2 by Optimizing Non-Native Interactions.
Autorzy :
B da Silva F; Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil.
M de Oliveira V; Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials , LNBio/CNPEM , Campinas , São Paulo 13083-970 , Brazil.
Sanches MN; Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil.
Contessoto VG; Brazilian Biorenewables National Laboratory - LNBR , Brazilian Center for Research in Energy and Materials - CNPEM , Campinas , São Paulo 13083-100 , Brazil.; Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States.
Leite VBP; Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil.
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Źródło :
Journal of chemical information and modeling [J Chem Inf Model] 2020 Feb 24; Vol. 60 (2), pp. 982-988. Date of Electronic Publication: 2019 Dec 19.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Drug Design*
Models, Molecular*
Peptides/*chemistry
Peptides/*metabolism
Plant Proteins/*chemistry
Plant Proteins/*metabolism
Hydrophobic and Hydrophilic Interactions ; Mutation ; Peptides/genetics ; Plant Proteins/genetics ; Protein Conformation ; Static Electricity
Czasopismo naukowe
Tytuł :
Modeling Chikungunya control strategies and Mayaro potential outbreak in the city of Rio de Janeiro.
Autorzy :
Dodero-Rojas E; Center for Theoretical Biological Physics, Rice University, Houston, TX, United States of America.; Theoretical and Computational Physics Laboratory, University of Costa Rica, San José, Costa Rica.
Ferreira LG; Department of Chemistry, Rice University, Houston, TX, United States of America.
Leite VBP; Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil.
Onuchic JN; Center for Theoretical Biological Physics, Rice University, Houston, TX, United States of America.; Department of Chemistry, Rice University, Houston, TX, United States of America.; Department of Physics & Astronomy, Rice University, Houston, TX, United States of America.; Department of Biosciences, Rice University, Houston, TX, United States of America.
Contessoto VG; Center for Theoretical Biological Physics, Rice University, Houston, TX, United States of America.; Brazilian Biorenewables National Laboratory - LNBR, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, SP, Brazil.
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Źródło :
PloS one [PLoS One] 2020 Jan 28; Vol. 15 (1), pp. e0222900. Date of Electronic Publication: 2020 Jan 28 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Models, Theoretical*
Chikungunya Fever/*epidemiology
Chikungunya virus/*pathogenicity
Animals ; Basic Reproduction Number ; Brazil/epidemiology ; Chikungunya Fever/virology ; Disease Outbreaks ; Epidemics/prevention & control ; Humans ; Insect Vectors/virology ; Mosquito Vectors/virology
Czasopismo naukowe
Tytuł :
Drift-diffusion (DrDiff) framework determines kinetics and thermodynamics of two-state folding trajectory and tunes diffusion models.
Autorzy :
Freitas FC; Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil.
Lima AN; Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil.
Contessoto VG; Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA.
Whitford PC; Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA.
Oliveira RJ; Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil.
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Źródło :
The Journal of chemical physics [J Chem Phys] 2019 Sep 21; Vol. 151 (11), pp. 114106.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
Non-Native Cooperative Interactions Modulate Protein Folding Rates.
Autorzy :
Bruno da Silva F; Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto - São Paulo 15054-000 , Brazil.
Contessoto VG; Brazilian Bioethanol Science and Technology Laboratory - CTBE , Campinas - São Paulo 13083-100 , Brazil.
de Oliveira VM; Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto - São Paulo 15054-000 , Brazil.
Clarke J; Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom.
Leite VBP; Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto - São Paulo 15054-000 , Brazil.
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Źródło :
The journal of physical chemistry. B [J Phys Chem B] 2018 Dec 06; Vol. 122 (48), pp. 10817-10824. Date of Electronic Publication: 2018 Nov 21.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Protein Folding*
Spectrin/*chemistry
Amino Acid Sequence ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Molecular Dynamics Simulation ; Mutation ; Protein Domains ; Sequence Alignment ; Spectrin/genetics ; Static Electricity
Czasopismo naukowe
Tytuł :
TKSA-MC: A web server for rational mutation through the optimization of protein charge interactions.
Autorzy :
Contessoto VG; Brazilian Bioethanol Science and Technology Laboratory - CTBE, Campinas, São Paulo, Brazil.; Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil.
de Oliveira VM; Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil.
Fernandes BR; Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil.
Slade GG; Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil.; Theoretical Biophysics Laboratory, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro - UFTM, Uberaba, Minas Gerais, Brazil.
Leite VBP; Department of Physics, Institute of Biosciences, Letters and Exact Sciences São Paulo State University - UNESP, São José do Rio Preto, São Paulo, Brazil.
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Źródło :
Proteins [Proteins] 2018 Nov; Vol. 86 (11), pp. 1184-1188. Date of Electronic Publication: 2018 Sep 28.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Proteins/*chemistry
Internet ; Monte Carlo Method ; Mutation ; Protein Conformation ; Protein Folding ; Protein Stability ; Proteins/genetics ; Software ; Static Electricity ; Thermodynamics
Czasopismo naukowe
Tytuł :
Cold Shock Protein A from Corynebacterium pseudotuberculosis: Role of Electrostatic Forces in the Stability of the Secondary Structure.
Autorzy :
Coronado MA; Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil.
Caruso IP; Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil.
Oliveira VM; Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil.
Contessoto VG; Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil.
Leite VBP; Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil.
Kawai LA; Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil.
Arni RK; Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil.
Eberle RJ; Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Rua Cristovao Colombo 2265, Sao Jose do Rio Preto-SP, 15054-000. Brazil.
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Źródło :
Protein and peptide letters [Protein Pept Lett] 2017; Vol. 24 (4), pp. 358-367.
Typ publikacji :
Journal Article
MeSH Terms :
Bacterial Proteins/*chemistry
Bacterial Proteins/*metabolism
Corynebacterium pseudotuberculosis/*chemistry
Corynebacterium pseudotuberculosis/metabolism ; Hydrogen/chemistry ; Hydrogen/metabolism ; Hydrogen-Ion Concentration ; Models, Molecular ; Protein Binding ; Protein Stability ; Protein Structure, Secondary ; Recombinant Proteins/chemistry ; Recombinant Proteins/metabolism ; Sodium/chemistry ; Sodium/metabolism ; Static Electricity
Czasopismo naukowe
Tytuł :
NTL9 Folding at Constant pH: The Importance of Electrostatic Interaction and pH Dependence.
Autorzy :
Contessoto VG; Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP) , São José do Rio Preto, São Paulo 15054-000, Brazil.
de Oliveira VM; Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP) , São José do Rio Preto, São Paulo 15054-000, Brazil.
de Carvalho SJ; Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP) , São José do Rio Preto, São Paulo 15054-000, Brazil.
Oliveira LC; Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP) , São José do Rio Preto, São Paulo 15054-000, Brazil.
Leite VB; Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP) , São José do Rio Preto, São Paulo 15054-000, Brazil.
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Źródło :
Journal of chemical theory and computation [J Chem Theory Comput] 2016 Jul 12; Vol. 12 (7), pp. 3270-7. Date of Electronic Publication: 2016 Jul 01.
Typ publikacji :
Journal Article
MeSH Terms :
Static Electricity*
Protein Folding/*drug effects
Hydrogen-Ion Concentration ; Models, Molecular
Czasopismo naukowe
Tytuł :
Analyzing the effect of homogeneous frustration in protein folding.
Autorzy :
Contessoto VG; Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, Sao José do Rio Preto, São Paulo, 15054-000, Brazil.
Lima DT
Oliveira RJ
Bruni AT
Chahine J
Leite VB
Pokaż więcej
Źródło :
Proteins [Proteins] 2013 Oct; Vol. 81 (10), pp. 1727-37. Date of Electronic Publication: 2013 Jul 22.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Molecular Dynamics Simulation*
Protein Folding*
Proteins*/chemistry
Proteins*/metabolism
Least-Squares Analysis ; Multivariate Analysis ; Principal Component Analysis ; Thermodynamics
Czasopismo naukowe
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