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检索条件"机构=Ph.D. Program in Chemistry and PhD program in Biochemistry"
40 条 记 录,以下是1-10 订阅
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Ethylene Glycol-Manipulated Syntheses of Calcium Carbonate Particles and dNA Capsules toward Efficient ATP-Responsive Cargo Release
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ACS Applied Bio Materials 2023年 第8期6卷 3351-3360页
作者: Lin, Yu-Hsuan Singuru, Murali Mohana Rao Marpaung, david Septian Sumanto Liao, Wei-Ching Chuang, Min-Chieh Department of Chemistry Tunghai University Taichung407224 Taiwan International Ph.D. Program in Biomedical and Materials Science Tunghai University Taichung407224 Taiwan Department of Biosystems Engineering Institut Teknologi Sumatera Lampung Selatan35365 Indonesia Institute of Biochemistry and Molecular Biology National Yang Ming Chiao Tung University Taipei112304 Taiwan
Cargo molecule-encapsulated dNA capsules synthesized with a solid sacrificial template have elicited significant interest in the last decade and have been used for active materials in applications ranging from biosens... 详细信息
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Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer with Coordinate Swapping Method
arXiv
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arXiv 2024年
作者: Gallicchio, Emilio Department of Chemistry and Biochemistry Brooklyn College The City University of New York New YorkNY11210 United States Ph.D. Program in Chemistry The Graduate Center The City University of New York New YorkNY10016 United States Ph.D. Program in Biochemistry The Graduate Center The City University of New York New YorkNY10016 United States
We present the Alchemical Transfer with Coordinate Swapping (ATS) method to enable the calculation of the relative binding free energies between large congeneric ligands and single-point mutant peptides to protein rec... 详细信息
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Potential distribution Theory of Alchemical Transfer
arXiv
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arXiv 2024年
作者: Azimi, Solmaz Gallicchio, Emilio Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Program in Chemistry The Graduate Center of the City University of New York New YorkNY United States
We present an analytical description of the Alchemical Transfer Method (ATM) for molecular binding using the Potential distribution Theory (PdT) formalism. ATM models the binding free energy by mapping the bound and u... 详细信息
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A disordered linker in the Polycomb protein Polyhomeotic tunes phase separation and oligomerization
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Molecular Cell 2025年 第11期85卷 2128-2146.e15页
作者: Gemeinhardt, Tim M. Regy, Roshan M. phan, Tien M. Pal, Nanu Sharma, Jyoti Senkovich, Olga Mendiola, Andrea J. Ledterman, Heather J. Henrickson, Amy Lopes, daniel Kapoor, Utkarsh Bihani, Ashish Sihou, djamouna Kim, Young C. Jeruzalmi, david demeler, Borries Kim, Chongwoo A. Mittal, Jeetain Francis, Nicole J. Montreal Clinical Research Institute (IRCM) Montreal QC Canada Division of Experimental Medicine McGill University Montreal QC Canada Artie McFerrin Department of Chemical Engineering Texas A&M University College Station TX United States Department of Biochemistry and Molecular Medicine University of Montreal Montreal QC Canada Department of Biochemistry and Molecular Genetics Midwestern University Glendale AZ United States Department of Chemistry and Biochemistry The University of Lethbridge Lethbridge AB Canada Department of Chemistry and Biochemistry City College of New York New York NY United States Department of Chemical and Biomedical Engineering University of Wyoming Laramie WY United States Center for Materials Physics and Technology Naval Research Laboratory Washington DC United States Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New York NY United States Ph.D. Program in Biology The Graduate Center of the City University of New York New York NY United States Ph.D. Program in Chemistry The Graduate Center of the City University of New York New York NY United States Department of Chemistry and Biochemistry University of Montana Missoula MT United States Department of Chemistry Texas A&M University College Station TX United States Interdisciplinary Graduate Program in Genetics and Genomics Texas A&M University College Station TX United States
Biomolecular condensates are increasingly recognized as key regulators of chromatin organization, yet how their formation and properties arise from protein sequences remains incompletely understood. Cross-species comp... 详细信息
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Performance and Analysis of the Alchemical Transfer Method for Binding Free Energy Predictions of diverse Ligands
arXiv
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arXiv 2023年
作者: Chen, Lieyang Wu, Yujie Wu, Chuanjie Silveira, Ana Sherman, Woody Xu, Huafeng Gallicchio, Emilio Roivant Sciences 151 W 42nd Street 15th Floor New YorkNY10036 United States Atommap Corporation New YorkNY10017 United States Psivant Therapeutics 451 D Street BostonMA02210 United States Department of Chemistry Brooklyn College of the City University of New York New YorkNY United States Ph.D. Program in Chemistry The Graduate Center of the City University of New York New YorkNY United States Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States
The Alchemical Transfer Method (ATM) is herein validated against the relative binding free energies of a diverse set of protein-ligand complexes. We employed a streamlined setup workflow, a bespoke force field, and th... 详细信息
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Environmental Assessment in Fine Jewelry in the U.S.-Mexico's Paso del Norte Region: A Qualitative Study Via X-Ray Fluorescence Spectroscopy
SSRN
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SSRN 2022年
作者: Lerma, Maricarmen Banu, Kazi Saima Gardea-Torresdey, Jorge L. Environmental Sciences and Engineering Ph.D. Program The University of Texas at El Paso 500 West University Avenue El PasoTX79968 United States Department of Chemistry and Biochemistry The University of Texas at El Paso 500 West University Avenue El PasoTX79968 United States
Heavy metal contamination in raw materials has spread widely in the United States. The high increased number of recalls in consumer products and the lack of stricter regulations in the raw materials to be used in the ... 详细信息
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Relative binding free energy calculations for ligands with diverse scaffolds with the alchemical transfer method
arXiv
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arXiv 2021年
作者: Azimi, Solmaz Khuttan, Sheenam Wu, Joe Z. Pal, Rajat K. Gallicchio, Emilio Department of Chemistry Brooklyn College of the City University of New York New YorkNY United States Ph.D. Program in Biochemistry Graduate Center of the City University of New York New YorkNY United States Ph.D. Program in Chemistry Graduate Center of the City University of New York New YorkNY United States Roivant Sciences BostonMA United States
We present an extension of Alchemical Transfer Method (ATM) for the estimation of relative binding free energies of molecular complexes applicable to conventional as well as scaffold-hopping alchemical transformations... 详细信息
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Alchemical transfer approach to absolute binding free energy estimation
arXiv
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arXiv 2021年
作者: Wu, Joe Z. Azimi, Solmaz Khuttan, Sheenam deng, Nanjie Gallicchio, Emilio Department of Chemistry Brooklyn College of the City University of New York New YorkNY United States Ph.D. Program in Chemistry The Graduate Center of the City University of New York New YorkNY United States Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Department of Chemistry and Physical Sciences Pace University New YorkNY10038 United States
The Alchemical Transfer Method (ATM) for the calculation of standard binding free energies of non-covalent molecular complexes is presented. The method is based on a coordinate displacement perturbation of the ligand ... 详细信息
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AmberTools
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Journal of Chemical Information and Modeling 2023年 第20期63卷 6183-6191页
作者: Case, david A. Aktulga, Hasan Metin Belfon, Kellon Cerutti, david S. Cisneros, G. Andrés Cruzeiro, Vinícius Wilian d. Forouzesh, Negin Giese, Timothy J. Götz, Andreas W. Gohlke, Holger Izadi, Saeed Kasavajhala, Koushik Kaymak, Mehmet C. King, Edward Kurtzman, Tom Lee, Tai-Sung Li, Pengfei Liu, Jian Luchko, Tyler Luo, Ray Manathunga, Madushanka Machado, Matias R. Nguyen, Hai Minh O’Hearn, Kurt A. Onufriev, Alexey V. Pan, Feng Pantano, Sergio Qi, Ruxi Rahnamoun, Ali Risheh, Ali Schott-Verdugo, Stephan Shajan, Akhil Swails, Jason Wang, Junmei Wei, Haixin Wu, Xiongwu Wu, Yongxian Zhang, Shi Zhao, Shiji Zhu, Qiang Cheatham, Thomas E. Roe, daniel R. Roitberg, Adrian Simmerling, Carlos York, darrin M. Nagan, Maria C. Merz, Kenneth M. Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States Department of Computer Science and Engineering Michigan State University East LansingMI48824-1322 United States FOG Pharmaceuticals Inc. CambridgeMA02140 United States Psivant 451 D Street Suite 205 BostonMA02210 United States Department of Physics Department of Chemistry and Biochemistry University of Texas at Dallas RichardsonTX75801 United States Department of Chemistry and The PULSE Institute Stanford University StanfordCA94305 United States Department of Computer Science California State University Los AngelesCA90032 United States Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States San Diego Supercomputer Center University of California San Diego La Jolla CA92093-0505 United States Institute for Pharmaceutical and Medicinal Chemistry Heinrich Heine University Düsseldorf Düsseldorf40225 Germany Forschungszentrum Jülich GmbH Jülich52425 Germany Pharmaceutical Development Genentech Inc. South San FranciscoCA94080 United States Laufer Center for Physical and Quantitative Biology Department of Chemistry Stony Brook University Stony BrookNY11794 United States Departments of Molecular Biology and Biochemistry Chemical and Biomolecular Engineering Materials Science and Engineering and Biomedical Engineering Graduate Program in Chemical and Materials Physics University of California IrvineCA92697 United States Ph.D. Programs in Chemistry Biochemistry and Biology The Graduate Center of the City University of New York 365 Fifth Avenue New YorkNY10016 United States Department of Chemistry Lehman College 250 Bedford Park Blvd West BronxNY10468 United States Department of Chemistry and Biochemistry Loyola University Chicago ChicagoIL60660 United States Beijing National Laboratory for Molecular Science
AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note. ... 详细信息
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Integrating Computation, Experiment, and Machine Learning in the design of Peptide-Based Supramolecular Materials and Systems
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Angewandte Chemie 2023年 第18期135卷
作者: Maithreyi Ramakrishnan Alexander van Teijlingen Tell Tuttle R. V. Ulijn Advanced Science Research Center (ASRC) at the Graduate Center City University of New York (CUNY) New York NY 10031 USA Department of Chemistry Hunter College The City University of New York New York NY 10065 USA Ph.D. Program in Chemistry The Graduate Center of the City University of New York New York NY 10016 USA Pure and Applied Chemistry University of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK Ph.D. Program in Chemistry and PhD program in Biochemistry The Graduate Center of the City University of New York New York NY 10016 USA
Interest in peptide-based supramolecular materials has grown extensively since the 1980s and the application of computational methods has paralleled this. These methods contribute to the understanding of experimental ... 详细信息
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