Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity
Zhang, She, Li, Hongchun, Krieger, James M, Bahar, Ivet
Published in Molecular biology and evolution (01.09.2019)
Published in Molecular biology and evolution (01.09.2019)
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Journal Article
Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations
Lee, Ji Young, Krieger, James M., Li, Hongchun, Bahar, Ivet
Published in Protein science (01.01.2020)
Published in Protein science (01.01.2020)
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Journal Article
A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro
Cheng, Mary Hongying, Porritt, Rebecca A., Rivas, Magali Noval, Krieger, James M., Ozdemir, Asli Beyza, Garcia, Gustavo, Arumugaswami, Vaithilingaraja, Fries, Bettina C., Arditi, Moshe, Bahar, Ivet
Published in Structure (London) (02.09.2021)
Published in Structure (London) (02.09.2021)
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Journal Article
Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing
Krieger, James M, Sorzano, Carlos Oscar S, Carazo, Jose Maria
Published in International journal of molecular sciences (18.09.2023)
Published in International journal of molecular sciences (18.09.2023)
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Journal Article
Conformational Recognition of an Intrinsically Disordered Protein
Krieger, James M., Fusco, Giuliana, Lewitzky, Marc, Simister, Philip C., Marchant, Jan, Camilloni, Carlo, Feller, Stephan M., De Simone, Alfonso
Published in Biophysical journal (15.04.2014)
Published in Biophysical journal (15.04.2014)
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Journal Article
Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor
Herguedas, Beatriz, Kohegyi, Bianka K., Dohrke, Jan-Niklas, Watson, Jake F., Zhang, Danyang, Ho, Hinze, Shaikh, Saher A., Lape, Remigijus, Krieger, James M., Greger, Ingo H.
Published in Nature communications (08.02.2022)
Published in Nature communications (08.02.2022)
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Journal Article
Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions
Cheng, Mary Hongying, Krieger, James M., Banerjee, Anupam, Xiang, Yufei, Kaynak, Burak, Shi, Yi, Arditi, Moshe, Bahar, Ivet
Published in iScience (18.03.2022)
Published in iScience (18.03.2022)
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Journal Article
Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods
Kaynak, Burak T, Krieger, James M, Dudas, Balint, Dahmani, Zakaria L, Costa, Mauricio G S, Balog, Erika, Scott, Ana Ligia, Doruker, Pemra, Perahia, David, Bahar, Ivet
Published in Frontiers in molecular biosciences (04.02.2022)
Published in Frontiers in molecular biosciences (04.02.2022)
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Journal Article
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
Zhang, She, Krieger, James M, Zhang, Yan, Kaya, Cihan, Kaynak, Burak, Mikulska-Ruminska, Karolina, Doruker, Pemra, Li, Hongchun, Bahar, Ivet
Published in Bioinformatics (Oxford, England) (25.10.2021)
Published in Bioinformatics (Oxford, England) (25.10.2021)
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Journal Article
Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor
Zhang, Danyang, Ivica, Josip, Krieger, James M., Ho, Hinze, Yamashita, Keitaro, Stockwell, Imogen, Baradaran, Rozbeh, Cais, Ondrej, Greger, Ingo H.
Published in Nature (London) (28.09.2023)
Published in Nature (London) (28.09.2023)
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Journal Article
WatFinder: a ProDy tool for protein–water interactions
Krieger, James M, Doljanin, Frane, Bogetti, Anthony T, Zhang, Feng, Manivarma, Thiliban, Bahar, Ivet, Mikulska-Ruminska, Karolina
Published in Bioinformatics (Oxford, England) (02.08.2024)
Published in Bioinformatics (Oxford, England) (02.08.2024)
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Journal Article
GPCR kinases generate an APH1A phosphorylation barcode to regulate amyloid-β generation
Todd, Nicholas K., Huang, Yunhong, Lee, Ji Young, Doruker, Pemra, Krieger, James M., Salisbury, Ryan, MacDonald, Matthew, Bahar, Ivet, Thathiah, Amantha
Published in Cell reports (Cambridge) (19.07.2022)
Published in Cell reports (Cambridge) (19.07.2022)
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Computational biophysics meets cryo‐EM revolution in the search for the functional dynamics of biomolecular systems
Costa, Mauricio G. S., Gur, Mert, Krieger, James M., Bahar, Ivet
Published in Wiley interdisciplinary reviews. Computational molecular science (01.01.2024)
Published in Wiley interdisciplinary reviews. Computational molecular science (01.01.2024)
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Journal Article
Prody's latest advancements: Gaining insights into protein-protein and protein-water interactions, and their role in protein dynamics
Mikulska-Ruminska, Karolina, Doljanin, Frane, Krieger, James M., Cao, Xin, Wu, Gary, Banerjee, Anupam, Simmerling, Carlos, Coutsias, Evangelos A., Bahar, Ivet
Published in Biophysical journal (08.02.2024)
Published in Biophysical journal (08.02.2024)
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Journal Article
Scipion flexibility hub and Scipion chem: New frameworks coupling computational biophysics of protein dynamics and virtual screening to cryo-electron microscopy
Krieger, James M., Herreros, David, Hoyo, Daniel del, Fonseca, Yunior, Gragera, Marcos, Mata, Carlos P., Lomas, Alba, Ulzurrun, Eugenia, Campillo, Nuria E., Conesa, Pablo, Sorzano, Carlos Oscar S., Carazo, Jose Maria
Published in Biophysical journal (08.02.2024)
Published in Biophysical journal (08.02.2024)
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Journal Article
Dynamics of AMPA Receptors from Simulations and Electron Microscopy
Krieger, James M., Herguedas, Béatriz, Singh, Bishal, Lee, Jiyoung, Kaynak, Burak, Greger, Ingo, Bahar, Ivet
Published in Biophysical journal (15.02.2019)
Published in Biophysical journal (15.02.2019)
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Journal Article
The Impact of Menu Labeling on Fast-Food Purchases for Children and Parents
Tandon, Pooja S., MD, MPH, Zhou, Chuan, PhD, Chan, Nadine L., PhD, MPH, Lozano, Paula, MD, MPH, Couch, Sarah C., PhD, RD, Glanz, Karen, PhD, MPH, Krieger, James, MD, MPH, Saelens, Brian E., PhD
Published in American journal of preventive medicine (01.10.2011)
Published in American journal of preventive medicine (01.10.2011)
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Journal Article
Nutrition-Labeling Regulation Impacts on Restaurant Environments
Saelens, Brian E., PhD, Chan, Nadine L., PhD, MPH, Krieger, James, MD, MPH, Nelson, Young, BA, Boles, Myde, PhD, MBA, Colburn, Trina A., PhD, Glanz, Karen, PhD, MPH, Ta, Myduc L., PhD, MPH, Bruemmer, Barbara, PhD, RD
Published in American journal of preventive medicine (01.11.2012)
Published in American journal of preventive medicine (01.11.2012)
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