Search Results - "Hall, David R."

The ClusPro web server for protein–protein docking by Kozakov, Dima, Hall, David R, Xia, Bing, Porter, Kathryn A, Padhorny, Dzmitry, Yueh, Christine, Beglov, Dmitri, Vajda, Sandor

“…ClusPro is a web server that performs rigid-body docking of two proteins by sampling billions of conformations. Low-energy docked structures are clustered, and…”
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How good is automated protein docking? by Kozakov, Dima, Beglov, Dmitri, Bohnuud, Tanggis, Mottarella, Scott E., Xia, Bing, Hall, David R., Vajda, Sandor

“…ABSTRACT The protein docking server ClusPro has been participating in critical assessment of prediction of interactions (CAPRI) since its introduction in 2004…”
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New additions to the ClusPro server motivated by CAPRI by Vajda, Sandor, Yueh, Christine, Beglov, Dmitri, Bohnuud, Tanggis, Mottarella, Scott E., Xia, Bing, Hall, David R., Kozakov, Dima

“…ABSTRACT The heavily used protein–protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based…”
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Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs by Whitty, Adrian, Zhong, Mengqi, Viarengo, Lauren, Beglov, Dmitri, Hall, David R., Vajda, Sandor

“…•‘Chameleonic’ behavior is known to be important for the bioavailability of certain macrocyclic drugs.•We show that some degree of chameleonic behavior is…”
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The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins by Kozakov, Dima, Grove, Laurie E, Hall, David R, Bohnuud, Tanggis, Mottarella, Scott E, Luo, Lingqi, Xia, Bing, Beglov, Dmitri, Vajda, Sandor

“…This protocol describes the FTMap family of web servers for determining and characterizing ligand-binding hot spots of macromolecules, including FTSite for…”
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The hypertensive disorders of pregnancy: ISSHP classification, diagnosis & management recommendations for international practice by Brown, Mark A., Magee, Laura A., Kenny, Louise C., Karumanchi, S. Ananth, McCarthy, Fergus P, Saito, Shigeru, Hall, David R., Warren, Charlotte E., Adoyi, Gloria, Ishaku, Salisu

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The 2021 International Society for the Study of Hypertension in Pregnancy classification, diagnosis & management recommendations for international practice by Magee, Laura A, Brown, Mark A., Hall, David R., Gupte, Sanjay, Hennessy, Annemarie, Karumanchi, S. Ananth, Kenny, Louise C., McCarthy, Fergus, Myers, Jenny, Poon, Liona C., Rana, Sarosh, Saito, Shigeru, Staff, Anne Cathrine, Tsigas, Eleni, von Dadelszen, Peter

“…•This updates the 2018 ISSHP guidelines, and feedback is invited (info@isshp.org).•Angiogenic imbalance is uteroplacental dysfunction when…”
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Potent cross-reactive antibodies following Omicron breakthrough in vaccinees by Nutalai, Rungtiwa, Zhou, Daming, Tuekprakhon, Aekkachai, Ginn, Helen M., Supasa, Piyada, Liu, Chang, Huo, Jiandong, Mentzer, Alexander J., Duyvesteyn, Helen M.E., Dijokaite-Guraliuc, Aiste, Skelly, Donal, Ritter, Thomas G., Amini, Ali, Bibi, Sagida, Adele, Sandra, Johnson, Sile Ann, Constantinides, Bede, Webster, Hermione, Temperton, Nigel, Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Crook, Derrick, Pollard, Andrew J., Lambe, Teresa, Goulder, Philip, Paterson, Neil G., Williams, Mark A., Hall, David R., Mongkolsapaya, Juthathip, Fry, Elizabeth E., Dejnirattisai, Wanwisa, Ren, Jingshan, Stuart, David I., Screaton, Gavin R.

“…Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD…”
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Exploring the structural origins of cryptic sites on proteins by Beglov, Dmitri, Hall, David R., Wakefield, Amanda E., Luo, Lingqi, Allen, Karen N., Kozakov, Dima, Whitty, Adrian, Vajda, Sandor

“…Molecular dynamics (MD) simulations of proteins reveal the existence of many transient surface pockets; however, the factors determining what small subset of…”
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Early postpartum HbA1c after hyperglycemia first detected in pregnancy-Imperfect but not without value by Coetzee, Ankia, Hall, David R, van de Vyver, Mari, Conradie, Magda

“…South African women of childbearing age are disproportionally affected by obesity and at significant risk of Type 2 Diabetes Mellitus (T2DM). Unless pregnant,…”
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Structural conservation of druggable hot spots in protein–protein interfaces by Kozakov, Dima, Hall, David R, Chuang, Gwo-Yu, Cencic, Regina, Brenke, Ryan, Grove, Laurie E, Beglov, Dmitri, Pelletier, Jerry, Whitty, Adrian, Vajda, Sandor

“…Despite the growing number of examples of small-molecule inhibitors that disrupt protein–protein interactions (PPIs), the origin of druggability of such…”
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Application of asymmetric statistical potentials to antibody―protein docking by BRENKE, Ryan, HALL, David R, CHUANG, Gwo-Yu, COMEAU, Stephen R, BOHNUUD, Tanggis, BEGLOV, Dmitri, SCHUELER-FURMAN, Ora, VAJDA, Sandor, KOZAKOV, Dima

“…An effective docking algorithm for antibody-protein antigen complex prediction is an important first step toward design of biologics and vaccines. We have…”
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The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants by Liu, Chang, Zhou, Daming, Nutalai, Rungtiwa, Duyvesteyn, Helen M.E., Tuekprakhon, Aekkachai, Ginn, Helen M., Dejnirattisai, Wanwisa, Supasa, Piyada, Mentzer, Alexander J., Wang, Beibei, Case, James Brett, Zhao, Yuguang, Skelly, Donal T., Chen, Rita E., Johnson, Sile Ann, Ritter, Thomas G., Mason, Chris, Malik, Tariq, Temperton, Nigel, Paterson, Neil G., Williams, Mark A., Hall, David R., Clare, Daniel K., Howe, Andrew, Goulder, Philip J.R., Fry, Elizabeth E., Diamond, Michael S., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., Screaton, Gavin R.

“…Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the…”
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Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19 by Kozakov, Dima, Hall, David R., Beglov, Dmitri, Brenke, Ryan, Comeau, Stephen R., Shen, Yang, Li, Keyong, Zheng, Jiefu, Vakili, Pirooz, Paschalidis, Ioannis Ch, Vajda, Sandor

“…Our approach to protein—protein docking includes three main steps. First, we run PIPER, a rigid body docking program based on the Fast Fourier Transform (FFT)…”
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Prostaglandin E2 Signaling Mediates Oenocytoid Immune Cell Function and Lysis, Limiting Bacteria and Plasmodium Oocyst Survival in Anopheles gambiae by Kwon, Hyeogsun, Hall, David R., Smith, Ryan C.

“…Lipid-derived signaling molecules known as eicosanoids have integral roles in mediating immune and inflammatory processes across metazoans. This includes the…”
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Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein–Protein Interfaces by Zerbe, Brandon S, Hall, David R, Vajda, Sandor, Whitty, Adrian, Kozakov, Dima

“…In the context of protein–protein interactions, the term “hot spot” refers to a residue or cluster of residues that makes a major contribution to the binding…”
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Ligand deconstruction: Why some fragment binding positions are conserved and others are not by Kozakov, Dima, Hall, David R., Jehle, Stefan, Luo, Lingqi, Ochiana, Stefan O., Jones, Elizabeth V., Pollastri, Michael, Allen, Karen N., Whitty, Adrian, Vajda, Sandor

“…Significance Fragment-based drug discovery (FBDD), in which initial screening is done with low-molecular-weight compounds called fragments, relies on the…”
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Surveillance and genetic data support the introduction and establishment of Aedes albopictus in Iowa, USA by Hall, David R., Tokarz, Ryan E., Field, Eleanor N., Smith, Ryan C.

“…Aedes albopictus is a competent vector of several arboviruses that has spread throughout the United States over the last three decades. With the emergence of…”
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Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F by Cencic, Regina, Hall, David R., Robert, Francis, Du, Yuhong, Min, Jaeki, Li, Lian, Qui, Min, Lewis, Iestyn, Kurtkaya, Serdar, Dingledine, Ray, Fu, Haian, Kozakov, Dima, Vajda, Sandor, Pelletier, Jerry, Housman, David E.

“…Deregulation of cap-dependent translation is associated with cancer initiation and progression. The rate-limiting step of protein synthesis is the loading of…”
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Interaction Energetics and Druggability of the Protein–Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2) by Zhong, Mengqi, Lynch, Andrew, Muellers, Samantha N, Jehle, Stefan, Luo, Lingqi, Hall, David R, Iwase, Reina, Carolan, James P, Egbert, Megan, Wakefield, Amanda, Streu, Kristina, Harvey, Christine M, Ortet, Paula C, Kozakov, Dima, Vajda, Sandor, Allen, Karen N, Whitty, Adrian

“…Development of small molecule inhibitors of protein–protein interactions (PPIs) is hampered by our poor understanding of the druggability of PPI target sites…”
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