Search Results - "Seffernick, Justin T."

Hybrid methods for combined experimental and computational determination of protein structure by Seffernick, Justin T, Lindert, Steffen

“…Knowledge of protein structure is paramount to the understanding of biological function, developing new therapeutics, and making detailed mechanistic…”
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Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling by Drake, Zachary C., Seffernick, Justin T., Lindert, Steffen

“…Covalent labeling (CL) in combination with mass spectrometry can be used as an analytical tool to study and determine structural properties of protein-protein…”
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Relative interfacial cleavage energetics of protein complexes revealed by surface collisions by Harvey, Sophie R., Seffernick, Justin T., Quintyn, Royston S., Song, Yang, Ju, Yue, Yan, Jing, Sahasrabuddhe, Aniruddha N., Norris, Andrew, Zhou, Mowei, Behrman, Edward J., Lindert, Steffen, Wysocki, Vicki H.

“…To fulfill their biological functions, proteins must interact with their specific binding partners and often function as large assemblies composed of multiple…”
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Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction by Turzo, SM Bargeen Alam, Seffernick, Justin T., Rolland, Amber D., Donor, Micah T., Heinze, Sten, Prell, James S., Wysocki, Vicki H., Lindert, Steffen

“…Ion mobility (IM) mass spectrometry provides structural information about protein shape and size in the form of an orientationally-averaged collision…”
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Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data by Seffernick, Justin T, Harvey, Sophie R, Wysocki, Vicki H, Lindert, Steffen

“…Recently, mass spectrometry (MS) has become a viable method for elucidation of protein structure. Surface-induced dissociation (SID), colliding multiply…”
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Protein Structure Prediction from NMR Hydrogen–Deuterium Exchange Data by Marzolf, Daniel R, Seffernick, Justin T, Lindert, Steffen

“…Amide hydrogen–deuterium exchange (HDX) has long been used to determine regional flexibility and binding sites in proteins; however, the data are too sparse…”
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Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder by Seffernick, Justin T, Ren, He, Kim, Stephanie S, Lindert, Steffen

“…Many proteins contain regions of intrinsic disorder, not folding into unique, stable conformations. Numerous experimental methods have been developed to…”
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Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application by Kim, Stephanie S, Seffernick, Justin T, Lindert, Steffen

“…Although many proteins necessitate well-folded structures to properly instigate their biological functions, a large fraction of functioning proteins contain…”
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Prediction of Intrinsic Disorder Using Rosetta ResidueDisorder and AlphaFold2 by He, Jiadi, Turzo, SM Bargeen Alam, Seffernick, Justin T., Kim, Stephanie S., Lindert, Steffen

“…The combination of deep learning and sequence data has transformed protein structure prediction and modeling, evidenced in the success of AlphaFold (AF). For…”
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Prediction of Protein Complex Structure Using Surface-Induced Dissociation and Cryo-Electron Microscopy by Seffernick, Justin T, Canfield, Shane M, Harvey, Sophie R, Wysocki, Vicki H, Lindert, Steffen

“…A variety of techniques involving the use of mass spectrometry (MS) have been developed to obtain structural information on proteins and protein complexes. One…”
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Protein structure prediction using residue-resolved protection factors from hydrogen-deuterium exchange NMR by Nguyen, Tung T., Marzolf, Daniel R., Seffernick, Justin T., Heinze, Sten, Lindert, Steffen

“…Hydrogen-deuterium exchange (HDX) measured by nuclear magnetic resonance (NMR) provides structural information for proteins relating to solvent accessibility…”
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Simulation of Energy-Resolved Mass Spectrometry Distributions from Surface-Induced Dissociation by Seffernick, Justin T., Turzo, SM Bargeen Alam, Harvey, Sophie R., Kim, Yongseok, Somogyi, Árpád, Marciano, Shir, Wysocki, Vicki H., Lindert, Steffen

“…Understanding the relationship between protein structure and experimental data is crucial for utilizing experiments to solve biochemical problems and…”
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Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver by Turzo, S M Bargeen Alam, Seffernick, Justin T, Lyskov, Sergey, Lindert, Steffen

“…Abstract Ion mobility coupled to mass spectrometry informs on the shape and size of protein structures in the form of a collision cross section (CCSIM)…”
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Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5‑Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA by Lu, Yanran, Vibhute, Sandip, Li, Linsen, Okumu, Antony, Ratigan, Steven C, Nolan, Sheri, Papa, Jonathan L, Mann, Chelsea A, English, Anthony, Chen, Anna, Seffernick, Justin T, Koci, Bryan, Duncan, Leonard R, Roth, Brieanna, Cummings, Jason E, Slayden, Richard A, Lindert, Steffen, McElroy, Craig A, Wozniak, Daniel J, Yalowich, Jack, Mitton-Fry, Mark J

“…Novel bacterial topoisomerase inhibitors (NBTIs) are among the most promising new antibiotics in preclinical/clinical development. We previously reported…”
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Dioxane-Linked Amide Derivatives as Novel Bacterial Topoisomerase Inhibitors against Gram-Positive Staphylococcus aureus by Lu, Yanran, Papa, Jonathan L, Nolan, Sheri, English, Anthony, Seffernick, Justin T, Shkolnikov, Nicholas, Powell, Josh, Lindert, Steffen, Wozniak, Daniel J, Yalowich, Jack, Mitton-Fry, Mark J

“…In recent years, novel bacterial topoisomerase inhibitors (NBTIs) have been developed as future antibacterials for treating multidrug-resistant bacterial…”
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Integrated Use of Biochemical, Native Mass Spectrometry, Computational, and Genome-Editing Methods to Elucidate the Mechanism of a Salmonella deglycase by Sengupta, Anindita, Wu, Jikang, Seffernick, Justin T., Sabag-Daigle, Anice, Thomsen, Nicholas, Chen, Tien-Hao, Capua, Angela Di, Bell, Charles E., Ahmer, Brian M.M., Lindert, Steffen, Wysocki, Vicki H., Gopalan, Venkat

“…Salmonellais a foodborne pathogen that causes annually millions of cases of salmonellosis globally, yet Salmonella-specific antibacterials are not available…”
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Development of Novel Bacterial Topoisomerase Inhibitors Assisted by Computational Screening by Powell, Joshua W., Mann, Chelsea A., Toth, Paul D., Nolan, Sheri, Steinert, Anja, Ove, Clarissa, Seffernick, Justin T., Wozniak, Daniel J., Kebriaei, Razieh, Lindert, Steffen, Osheroff, Neil, Yalowich, Jack C., Mitton-Fry, Mark J.

“…Multidrug-resistant bacterial infections pose an ever-evolving threat to public health. Since the outset of the antibacterial age, bacteria have developed a…”
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1,3-Dioxane-Linked Bacterial Topoisomerase Inhibitors with Enhanced Antibacterial Activity and Reduced hERG Inhibition by Li, Linsen, Okumu, Antony A, Nolan, Sheri, English, Anthony, Vibhute, Sandip, Lu, Yanran, Hervert-Thomas, Katherine, Seffernick, Justin T, Azap, Lovette, Cole, Serena L, Shinabarger, D, Koeth, Laura M, Lindert, Steffen, Yalowich, Jack C, Wozniak, Daniel J, Mitton-Fry, Mark J

“…The development of new therapies to treat methicillin-resistant Staphylococcus aureus (MRSA) is needed to counteract the significant threat that MRSA presents…”
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Prediction of protein complex structure using surface-induced dissociation and cryo-EM by Seffernick, Justin T., Canfield, Shane M., Harvey, Sophie R., Wysocki, Vicki H., Lindert, Steffen

“…A variety of techniques involving the use of mass spectrometry (MS) have been developed to obtain structural information on proteins and protein complexes. One…”
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Integrated Use of Biochemical, Native Mass Spectrometry, Computational, and Genome-Editing Methods to Elucidate the Mechanism of a deglycase by Sengupta, Anindita, Wu, Jikang, Seffernick, Justin T., Sabag-Daigle, Anice, Thomsen, Nicholas, Chen, Tien-Hao, Capua, Angela Di, Bell, Charles E., Ahmer, Brian M.M., Lindert, Steffen, Wysocki, Vicki H., Gopalan, Venkat

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