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检索条件"机构=Interdepartmental Graduate Program in Bioinformatics and Computational Biology"
178 条 记 录,以下是101-110 订阅
排序:
Void distributions reveal structural link between jammed packings and protein cores
arXiv
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arXiv 2018年
作者: Treado, John D. Mei, Zhe Regan, Lynne O'Hern, Corey S. Department of Mechanical Engineering & Materials Science Yale University New HavenCT06520 United States Integrated Graduate Program in Physical & Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Molecular Biophysics & Biochemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction φ ≈ 0.56, which is the same as dense, random pa... 详细信息
来源: 评论
Evaluation of drug repositioning by molecular docking of pharmaceutical resources available in the Brazilian healthcare system against SARS-CoV-2
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Informatics in Medicine Unlocked 2021年 23卷 100539页
作者: Grahl, Matheus V.C. Alcará, Allan M. Perin, Ana Paula A. Moro, Carlo F. Pinto, Éderson S.M. Feltes, Bruno C. Ghilardi, Isadora M. Rodrigues, Felipe V.F. Dorn, Marcio da Costa, Jaderson C. Norberto de Souza, Osmar Ligabue-Braun, Rodrigo Brain Institute of Rio Grande do Sul (BraIns) Pontifical Catholic University of Rio Grande do Sul Porto Alegre Brazil Graduate Program in Medicine and Health Sciences Pontifical Catholic University of Rio Grande do Sul Porto Alegre Brazil Graduate Program in Medicine Pediatrics and Child Health Pontifical Catholic University of Rio Grande do Sul Porto Alegre Brazil Graduate Program in Cellular and Molecular Biology Center of Biotechnology Federal University of Rio Grande do Sul RS Brazil Laboratory of Structural Bioinformatics and Computational Biology Institute of Informatics Federal University of Rio Grande do Sul RS Brazil Laboratory of Immunobiology and Immunogenetics Institute of Biosciences Federal University of Rio Grande do Sul RS Brazil School of Technology Pontifical Catholic University of Rio Grande do Sul Porto Alegre Brazil Department of Pharmacosciences and Graduate Program in Biosciences (PPGBio) Federal University of Health Sciences of Porto Alegre Porto Alegre Brazil
In 2020 SARS-CoV-2 reached pandemic status, reaching Brazil in mid-February. As of now, no specific drugs for treating the disease are available. In this work, the possibility of interaction between SARS-CoV-2 viral p... 详细信息
来源: 评论
Communicationmachine Learning-Based QSAR and LB-PaCS-MD Guided Design of SARs-CoV-2 Main Protease Inhibitors
SSRN
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SSRN 2024年
作者: Toopradab, Borwornlak Xie, Wanting Duan, Lian Hengphasatporn, Kowit Harada, Ryuhei Sinsulpsiri, Silpsiri Shigeta, Yasuteru Shi, Liyi Maitarad, Phornphimon Rungrotmongkol, Thanyada Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok10330 Thailand Center of Excellence in Biocatalyst and Sustainable Biotechnology Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok10330 Thailand Research Center of Nano Science and Technology Department of Chemistry College of Science Shanghai University Shanghai200444 China University of Tsukuba 1-1-1 Tennodai Ibaraki Tsukuba305-8577 Japan Graduate School of Pure and Applied Sciences University of Tsukuba 1-1-1 Tennodai Ibaraki305–8571 Japan Emerging Industries Institute Shanghai University Zhejiang Jiaxing314006 China
The global outbreak of the COVID-19 pandemic caused by the SARS-CoV-2 virus had led to profound respiratory health implications. This study focused on designing organoselenium-based inhibitors targeting the SARS-CoV-2... 详细信息
来源: 评论
Tessellated granular metamaterials with tunable elastic moduli
arXiv
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arXiv 2023年
作者: Pashine, Nidhi Wang, Dong Zhang, Jerry Patiballa, Sree Kalyan Witthaus, Sven Shattuck, Mark D. O’Hern, Corey S. Kramer-Bottiglio, Rebecca Department of Mechanical Engineering & Materials Science Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States Graduate Program in Computational Biology & Bioinformatics Yale University New HavenCT06520 United States Benjamin Levich Institute Physics Department The City College of the City University of New York New YorkNY10031 United States
Most granular packings possess shear moduli (G) that increase with the applied external pressure, and bulk moduli (B) that increase or remain constant with pressure. This paper presents "tessellated" granula... 详细信息
来源: 评论
帕博利珠单抗治疗伴脑转移NSCLC患者的一项非随机、开放Ⅱ期试验的长期随访结果和生物标志物分析
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中国肺癌杂志 2021年 第9期24卷 I0007-I0016页
作者: Sarah B GOLDBERG Kurt A SCHALPER Scott N GETTINGER Amit MAHAJAN Roy S HERBST Anne C CHANG Rogerio LILENBAUM Frederick H WILSON Sacit Bulent OMAY James B YU Lucia JILAVEANU Thuy TRAN Kira PAVLIK Elin ROWEN Heather GERRSH Annette KOMLO Richa GUPTA Hailey WYATT Matthew RIBEIRO Yuval KLUGER Geyu ZHOU Wei WEI Veronica L CHANG Harriet M KLUGER 董晓荣(翻译/校对) Department of Medicine(Medical Oncology) Yale School of MedicineNew HavenCTUSA Department of Pathology Yale School of MedicineNew HavenCTUSA Department of Radiology Yale School of MedicineNew HavenCTUSA Department of Neurosurgery Yale School of MedicineNew HavenCTUSA Department of Therapeutic Radiology Yale School of MedicineNew HavenCTUSA Interdepartmental Program in Computational Biology and Bioinformatics Yale School of MedicineNew HavenCTUSA Department of Biostatistics Yale School of Public HealthNew HavenCTUSA 华中科技大学同济医学院附属协和医院胸部肿瘤科
背景与目的我们开展了一项帕博利珠单抗用于伴未治疗脑转移的非小细胞肺癌(non-small cell lung cancer,NSCLC)或黑色素瘤患者的疗效和安全性的II期试验,旨在评估程序性死亡受体1(programmed cell death 1,PD-1)抑制剂在中枢神经系统(ce... 详细信息
来源: 评论
The impact of breast radiotherapy on the tumor genome and immune ecosystem
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Cell Reports 2025年 第5期44卷 115703页
作者: Aislyn Schalck Tuan Tran Jianzhuo Li Emi Sei Shanshan Bai Min Hu Jerome Lin Scott J. Bright Samuel Reddick Fei Yang Harsh Batra Alejandro Contreras Maria Gabriela Raso Michael C. Stauder Karen E. Hoffman Jay P. Reddy Kevin T. Nead Benjamin D. Smith Gabriel O. Sawakuchi Wendy A. Woodward Stephanie S. Watowich Jennifer K. Litton Isabelle Bedrosian Elizabeth A. Mittendorf Huong Le-Petross Nicholas E. Navin Simona F. Shaitelman Department of Systems Biology University of Texas MD Anderson Cancer Center Houston TX 77030 USA Graduate School of Biological Sciences University of Texas Houston TX 770303 USA Department of Radiation Physics University of Texas MD Anderson Cancer Center Houston TX 77030 USA Department of Breast Radiation Oncology University of Texas MD Anderson Cancer Center Houston TX 77030 USA Vanderbilt University School of Medicine Nashville TN 37232 USA Department of Translational Molecular Pathology University of Texas MD Anderson Cancer Center Houston TX 77030 USA Janssen China Research & Development Johnson&Johnson Shanghai 201210 China Department of Anatomical Pathology University of Texas MD Anderson Cancer Center Houston TX 77030 USA Department of Epidemiology University of Texas MD Anderson Cancer Center Houston TX 77030 USA Department of Immunology University of Texas MD Anderson Cancer Center Houston TX 77030 USA Department of Breast Medical Oncology University of Texas MD Anderson Cancer Center Houston TX 77030 USA Department of Breast Surgical Oncology University of Texas MD Anderson Cancer Center Houston TX 77030 USA Division of Breast Surgery Department of Surgery Brigham and Women’s Hospital Boston MA 02115 USA Breast Oncology Program Dana-Farber Brigham Cancer Center Boston MA 02115 USA Harvard Medical School Boston MA 02115 USA Department of Breast Imaging University of Texas MD Anderson Cancer Center Houston TX 77030 USA Department of Bioinformatics and Computational Biology University of Texas MD Anderson Cancer Center Houston TX 77030 USA
Radiotherapy is a pillar of breast cancer treatment; however, it remains unclear how radiotherapy modulates the tumor microenvironment. We investigated this question in a cohort of 20 patients with estrogen-receptor p... 详细信息
来源: 评论
Hypostatic jammed packings of frictionless nonspherical particles
arXiv
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arXiv 2017年
作者: VanderWerf, Kyle Jin, Weiwei Shattuck, Mark D. O'Hern, Corey S. Department of Physics Yale University New HavenCT06520 United States Benjamin Levich Institute and Physics Department City College of New York New YorkNY10031 United States Department of Mechanics and Engineering Science Peking University Beijing100871 China Department of Mechanical Engineering & Materials Science Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States
We perform computational studies of static packings of a variety of nonspherical particles including circulo-lines, circulo-polygons, ellipses, asymmetric dimers, dumbbells, and others to determine which shapes form p... 详细信息
来源: 评论
Assessment of scoring functions for computational models of protein-protein interfaces
arXiv
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arXiv 2024年
作者: Sumner, Jacob Meng, Grace Brandt, Naomi Grigas, Alex T. Córdoba, Andrés Shattuck, Mark D. O’Hern, Corey S. Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Chemistry Duke University DurhamNC27708 United States Department of Physics Duke University DurhamNC27708 United States Benjamin Levich Institute Physics Department City College of New York New YorkNY10031 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States
A goal of computational studies of protein-protein interfaces (PPIs) is to predict the binding site between two monomers that form a heterodimer. The simplest version of this problem is to rigidly re-dock the bound fo... 详细信息
来源: 评论
Current md forcefields fail to capture key features of protein structure and fluctuations: a case study of cyclophilin a and t4 lysozyme
arXiv
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arXiv 2020年
作者: Mei, Zhe Grigas, Alex T. Treado, John D. Corres, Gabriel Melendez Vuorte, Maisa Sammalkorpi, Maria Regan, Lynne Levine, Zachary A. O’Hern, Corey S. Department of Chemistry Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Biology UPR Humacao Puerto RicoHumacao00792 Puerto Rico Department of Chemistry and Materials Science School of Chemical Engineering Aalto University Aalto Finland Department of Bioproducts and Biosystems School of Chemical Engineering Aalto University Aalto Finland Institute of Quantitative Biology Biochemistry and Biotechnology Center for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Edinburgh United Kingdom Department of Pathology Yale School of Medicine New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, ... 详细信息
来源: 评论
Contact network changes in ordered and disordered disk packings
arXiv
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arXiv 2020年
作者: Tuckman, Philip J. VanderWerf, Kyle Yuan, Ye Zhang, Shiyun Zhang, Jerry Shattuck, Mark D. O’Hern, Corey S. Department of Physics Yale University New HavenCT06520 United States Department of Mechanics and Engineering Science College of Engineering Peking University Beijing100871 China Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Benjamin Levich Institute and Physics Department City College of New York New YorkNY10031 United States Department of Physics Yale University Department of Applied New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States
We investigate the mechanical response of packings of purely repulsive, frictionless disks to quasistatic deformations. The deformations include simple shear strain at constant packing fraction and at constant pressur... 详细信息
来源: 评论