Search Results - "Salsbury, Freddie"

Molecular dynamics simulations of protein dynamics and their relevance to drug discovery by Salsbury, Freddie R

“…Molecular dynamics simulations have become increasingly useful in studying biological systems of biomedical interest, and not just in the study of model or toy…”
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Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods by Wu, Dizhou, Salsbury, Freddie R.

“…Hydrogen bonds play a critical role in the folding and stability of proteins, such as proteins and nucleic acids, by providing strong and directional…”
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Light Chain Mutation Effects on the Dynamics of Thrombin by Wu, Dizhou, Xiao, Jiajie, Salsbury, Freddie R

“…Thrombin plays an important role in the process of hemostasis and blood coagulation. Studies in thrombin can help us find ways to treat cancer because thrombin…”
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Na + -binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling by Xiao, Jiajie, Salsbury, Freddie R

“…The monovalent sodium ion (Na+) is a critical modulator of thrombin. However, the mechanism of thrombin's activation by Na+ has been widely debated for more…”
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Thrombin - A Molecular Dynamics Perspective by Wu, Dizhou, Prem, Athul, Xiao, Jiajie, Salsbury, Freddie R

“…Thrombin is a crucial enzyme involved in blood coagulation, essential for maintaining circulatory system integrity and preventing excessive bleeding. However,…”
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Mechanistic insights into thrombin's switch between "slow" and "fast" forms by Xiao, Jiajie, Melvin, Ryan L, Salsbury, Freddie R

“…Thrombin is a multifunctional enzyme that plays an important role in blood coagulation, cell growth, and metastasis. Depending upon the binding of sodium ions,…”
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Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42) by Lu, Yan, Shi, Xiao-Feng, Salsbury, Jr, Freddie R, Derreumaux, Philippe

“…The formation of senile plaques in central neural system resulting from the aggregation of the amyloid β (Aβ) of 40 and 42 residues is one of the two hallmarks…”
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TREX1 as a Novel Immunotherapeutic Target by Hemphill, Wayne O, Simpson, Sean R, Liu, Mingyong, Salsbury, Jr, Freddie R, Hollis, Thomas, Grayson, Jason M, Perrino, Fred W

“…Mutations in the TREX1 3' → 5' exonuclease are associated with a spectrum of autoimmune disease phenotypes in humans and mice. Failure to degrade DNA activates…”
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Amyloid-β(29–42) Dimeric Conformations in Membranes Rich in Omega‑3 and Omega‑6 Polyunsaturated Fatty Acids by Lu, Yan, Shi, Xiao-Feng, Nguyen, Phuong H, Sterpone, Fabio, Salsbury, Freddie R, Derreumaux, Philippe

“…The omega-3 and omega-6 polyunsaturated fatty acids are two important components of cell membranes in human brains. When incorporated into phospholipids,…”
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Simulations suggest double sodium binding induces unexpected conformational changes in thrombin by Wu, Dizhou, Salsbury, Freddie R.

“…Thrombin is a Na + -activated serine protease existing in two forms targeted to procoagulant and anticoagulant activities, respectively. There is one Na +…”
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Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin by Xiao, Jiajie, Salsbury, Freddie R.

“…Thrombin is an attractive target for antithrombotic therapy due to its central role in thrombosis and hemostasis as well as its role in inducing tumor growth,…”
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Substrate recognition and near-cognate discrimination by the wobble-base modifying enzyme tRNA-isoleucine lysidine synthase (TilS) by Guinto, Ferdiemar C., Alexander, Rebecca W., Salsbury, Freddie R.

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Editorial: aims and scope update by Salsbury, Jr, Freddie R, Adnan, Mohd, Bishop, Thomas C, Chaires, Jonathan B, Hassan, Md Imtaiyaz

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Allosteric Modulation of Thrombin by Thrombomodulin: Insights from Logistic Regression and Statistical Analysis of Molecular Dynamics Simulations by Wu, Dizhou, Salsbury, Freddie R.

“…Thrombomodulin (TM), a transmembrane receptor integral to the anticoagulant pathway, governs thrombin’s substrate specificity via interaction with thrombin’s…”
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Experimentally Dissecting the Origins of Peroxiredoxin Catalysis by Nelson, Kimberly J, Perkins, Arden, Van Swearingen, Amanda E D, Hartman, Steven, Brereton, Andrew E, Parsonage, Derek, Salsbury, Jr, Freddie R, Karplus, P Andrew, Poole, Leslie B

“…Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases involved in oxidant defense and signal transduction. Despite much study, the precise roles of…”
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Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge by Melvin, Ryan L, Godwin, Ryan C, Xiao, Jiajie, Thompson, William G, Berenhaut, Kenneth S, Salsbury, Freddie R

“…As the length of molecular dynamics (MD) trajectories grows with increasing computational power, so does the importance of clustering methods for partitioning…”
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New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations by Lee, Michael S., Feig, Michael, Salsbury Jr, Freddie R., Brooks III, Charles L.

“…In a recent article (Lee, M. S.; Salsbury, F. R. Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606), we demonstrated that generalized Born (GB) theory…”
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Constant-pH molecular dynamics using continuous titration coordinates by Lee, Michael S., Salsbury Jr, Freddie R., Brooks III, Charles L.

“…In this work, we explore the question of whether pKa calculations based on a microscopic description of the protein and a macroscopic description of the…”
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Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning by Xiao, Jiajie, Melvin, Ryan L., Salsbury, Freddie R.

“…Thrombin is a key component for chemotherapeutic and antithrombotic therapy development. As the physiologic and pathologic roles of the light chain still…”
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Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator) by Godwin, Ryan C, Melvin, Ryan L, Gmeiner, William H, Salsbury, Freddie R

“…Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate…”
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