Search Results - "Zemla, T."

Large-scale application of free energy perturbation calculations for antibody design by Zhu, Fangqiang, Bourguet, Feliza A., Bennett, William F. D., Lau, Edmond Y., Arrildt, Kathryn T., Segelke, Brent W., Zemla, Adam T., Desautels, Thomas A., Faissol, Daniel M.

“…Alchemical free energy perturbation (FEP) is a rigorous and powerful technique to calculate the free energy difference between distinct chemical systems. Here…”
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LBA53 Alliance A021602: Phase III, double-blinded study of cabozantinib versus placebo for advanced neuroendocrine tumors (NET) after progression on prior therapy (CABINET) by Chan, J., Geyer, S., Ou, F-S., Knopp, M., Behr, S., Zemla, T., Acoba, J., Shergill, A., Wolin, E.M., Halfdanarson, T.R., Trikalinos, N., Konda, B., Vijayvergia, N., Dasari, N.A., Strosberg, J., Kohn, E.C., Kulke, M.H., O'Reilly, E.M., Meyerhardt, J.A.

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Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence by Borucki, Monica K, Collette, Nicole M, Coffey, Lark L, Van Rompay, Koen K A, Hwang, Mona H, Thissen, James B, Allen, Jonathan E, Zemla, Adam T

“…The question of how Zika virus (ZIKV) changed from a seemingly mild virus to a human pathogen capable of microcephaly and sexual transmission remains…”
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Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo by Collette, Nicole M, Lao, Victoria H I, Weilhammer, Dina R, Zingg, Barbara, Cohen, Shoshana D, Hwang, Mona, Coffey, Lark L, Grady, Sarah L, Zemla, Adam T, Borucki, Monica K

“…The 2014-2016 Zika virus (ZIKV) epidemic in the Americas resulted in large deposits of next-generation sequencing data from clinical samples. This resource was…”
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Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction by Chaudhury, Sidhartha, Abdulhameed, Mohamed Diwan M, Singh, Narender, Tawa, Gregory J, D'haeseleer, Patrik M, Zemla, Adam T, Navid, Ali, Zhou, Carol E, Franklin, Matthew C, Cheung, Jonah, Rudolph, Michael J, Love, James, Graf, John F, Rozak, David A, Dankmeyer, Jennifer L, Amemiya, Kei, Daefler, Simon, Wallqvist, Anders

“…In the future, we may be faced with the need to provide treatment for an emergent biological threat against which existing vaccines and drugs have limited…”
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StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase by Zemla, Adam T, Lang, Dorothy M, Kostova, Tanya, Andino, Raul, Ecale Zhou, Carol L

“…Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional…”
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Computational analysis of pathogen-borne metallo β-lactamases reveals discriminating structural features between B1 types by Cadag, Eithon, Vitalis, Elizabeth, Lennox, Kristin P, Zhou, Carol L Ecale, Zemla, Adam T

“…Genes conferring antibiotic resistance to groups of bacterial pathogens are cause for considerable concern, as many once-reliable antibiotics continue to see a…”
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PDBspheres: a method for finding 3D similarities in local regions in proteins by Zemla, Adam T, Allen, Jonathan E, Kirshner, Dan, Lightstone, Felice C

“…Abstract We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres…”
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Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases by Lang, Dorothy M, Zemla, A T, Zhou, C L Ecale

“…RNA-dependent RNA polymerase (RdRp) is essential to viral replication and is therefore one of the primary targets of countermeasures against these dangerous…”
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Randomized Trial of Mindfulness during Radiation Therapy by Sutton, E.A., Clark, M., Lester, S.C., Zemla, T., Davis, B.J., Choo, C.R., Corbin, K.S., Benzo, R.

“…Many patients receiving cancer treatment experience decreased quality of life (QoL). Evidence-based strategies are needed to mitigate this decline. Mindfulness…”
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A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV‑2 by Sandholtz, Sarah H., Drocco, Jeffrey A., Zemla, Adam T., Torres, Marisa W., Silva, Mary S., Allen, Jonathan E.

“…Minimizing the human and economic costs of the COVID-19 pandemic and future pandemics requires the ability to develop and deploy effective treatments for novel…”
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Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin by Zhou, Carol L. Ecale, Zemla, Adam T., Roe, Diana, Young, Malin, Lam, Marisa, Schoeniger, Joseph S., Balhorn, Rod

“…Motivation: Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers or other small…”
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Superconducting state in bromium halide at high pressure by Szczesniaka, R, Zemlab, T P, Szczesniakc, D

“…The thermodynamic properties of the superconducting state in bromium halide (HBr) compound have been analyzed in the framework of the Eliashberg formalism. In…”
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P-70 Outcomes following FGFR inhibitor therapy in patients with cholangiocarcinoma: Multi-center single institution cohort experience by Gile, J., Wookey, V., Zemla, T., Shi, Q., Bekaii-Saab, T., Tran, N., Mahipal, A.

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MannDB - a microbial database of automated protein sequence analyses and evidence integration for protein characterization by Zhou, Carol L Ecale, Lam, Marisa W, Smith, Jason R, Zemla, Adam T, Dyer, Matthew D, Kuczmarski, Thomas A, Vitalis, Elizabeth A, Slezak, Thomas R

“…MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving…”
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P-181 Outcomes of neoadjuvant and/or adjuvant treatment vs surgical resection alone for patients with cholangiocarcinoma: An inverse probability of treatment weighting with predictive nomogram by Hassan, H., Vanessa, W., Zemla, T., Yin, J., Prasai, K., Abdellatief, A., Katta, R., Tran, N., Mahipal, A.

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Radiation Therapy (RT) Quality Assurance (QA) Analysis of Alliance A021501: Preoperative mFOLFIRINOX or mFOLFIRINOX plus Hypofractionated Radiation Therapy for Borderline Resectable Adenocarcinoma of the Pancreas (PDAC) by Tchelebi, L., Smith, K.S., Shi, Q., Fitzgerald, T., Chuong, M.D., Zemla, T., O'Reilly, E., Meyerhardt, J., Koay, E.J., Leif, J.L., Katz, M.H.G., Herman, J.

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Structural re-alignment in an immunogenic surface region of ricin A chain by Zemla, Adam T, Ecale Zhou, Carol L

“…We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align…”
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Rapid development of nucleic acid diagnostics by Fitch, J.P., McCready, P.M., Gardner, S.N., Kuczmarski, T.A., Kurtz, S., Myers, R., Ott, L.L., Slezak, T.R., Vitalis, E.A., Zemla, A.T.

“…There has been a significant increase, fueled by technologies front the human genome project, in the availability of nucleic acid sequence information for…”
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Phase II trial of trifluridine/tipiracil (TAS-102) in patients with advanced refractory biliary tract cancer (BTC) by Chakrabarti, S., Zemla, T., Ou, F.-S., Fruth, B., Ahn, D., Borad, M.J., Hartgers, M.L., Wessling, J., Walkes, R.L., Alberts, S., McWilliams, R.R., Liu, M.C., Mahipal, A.

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