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Julie C. Mitchell - Publications

Affiliations: 
University of Wisconsin, Madison, Madison, WI 
Area:
Biochemistry, Computer Science, Oncology
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Hameedi MA, T Prates E, Garvin MR, Mathews II, Amos BK, Demerdash O, Bechthold M, Iyer M, Rahighi S, Kneller DW, Kovalevsky A, Irle S, Vuong VQ, Mitchell JC, Labbe A, et al. Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nature Communications. 13: 5285. PMID 36075915 DOI: 10.1038/s41467-022-32922-9  0.718
2022 Davidson R, Woods J, Effler TC, Thavappiragasam M, Mitchell JC, Parks JM, Sedova A. OpenMDlr: Parallel, open-source tools for general protein structure modeling and refinement from pairwise distances. Bioinformatics (Oxford, England). PMID 35512391 DOI: 10.1093/bioinformatics/btac307  0.332
2021 Hameedi MA, Prates ET, Garvin MR, Mathews I, Kirtley Amos B, Demerdash O, Bechthold M, Iyer M, Rahighi S, Kneller DW, Kovalevsky A, Irle S, Vuong VQ, Mitchell JC, Labbe A, et al. Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Biorxiv : the Preprint Server For Biology. PMID 34816264 DOI: 10.1101/2021.11.11.468228  0.717
2021 Mishra SK, Cooper CJ, Parks JM, Mitchell JC. Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes. The Journal of Physical Chemistry. B. PMID 34077660 DOI: 10.1021/acs.jpcb.0c11525  0.362
2020 Zhu X, Liu L, He J, Fang T, Xiong Y, Mitchell JC. iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots. Bmc Bioinformatics. 21: 289. PMID 32631222 DOI: 10.1186/s12859-020-03636-w  0.329
2020 Aranha MP, Spooner C, Demerdash O, Czejdo B, Smith JC, Mitchell JC. Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets. Biochimica Et Biophysica Acta. General Subjects. 129535. PMID 31954798 DOI: 10.1016/J.Bbagen.2020.129535  0.721
2019 Bortnov V, Tonelli M, Lee W, Lin Z, Annis DS, Demerdash ON, Bateman A, Mitchell JC, Ge Y, Markley JL, Mosher DF. Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum. Nature Communications. 10: 5612. PMID 31819058 DOI: 10.1038/S41467-019-13577-5  0.715
2019 Demerdash O, Shrestha UR, Petridis L, Smith JC, Mitchell JC, Ramanathan A. Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins. Frontiers in Molecular Biosciences. 6: 64. PMID 31475155 DOI: 10.3389/Fmolb.2019.00064  0.707
2018 Liu L, Xiong Y, Gao H, Wei DQ, Mitchell JC, Zhu X. dbAMEPNI: a database of alanine mutagenic effects for protein-nucleic acid interactions. Database : the Journal of Biological Databases and Curation. 2018. PMID 29688380 DOI: 10.1093/Database/Bay034  0.355
2016 Sukumar S, Zhu X, Ericksen SS, Mitchell JC. DBSI Server: DNA Binding Site Identifier. Bioinformatics (Oxford, England). PMID 27259543 DOI: 10.1093/Bioinformatics/Btw315  0.469
2016 Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidmann D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. Journal of Molecular Biology. PMID 26854760 DOI: 10.1016/J.Jmb.2016.01.029  0.742
2015 Alsop JD, Mitchell JC. Interolog interfaces in protein-protein docking. Proteins. PMID 25740680 DOI: 10.1002/Prot.24788  0.542
2015 Hatano H, Shaw J, Marquardt K, Zhang Z, Gauthier L, Chanteux S, Rossi B, Li D, Mitchell J, Kollnberger S. The D0 Ig-like domain plays a central role in the stronger binding of KIR3DL2 to B27 free H chain dimers. Journal of Immunology (Baltimore, Md. : 1950). 194: 1591-601. PMID 25582852 DOI: 10.4049/Jimmunol.1402214  0.338
2014 Lohman DC, Forouhar F, Beebe ET, Stefely MS, Minogue CE, Ulbrich A, Stefely JA, Sukumar S, Luna-Sánchez M, Jochem A, Lew S, Seetharaman J, Xiao R, Wang H, Westphall MS, ... ... Mitchell JC, et al. Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 111: E4697-705. PMID 25339443 DOI: 10.1073/Pnas.1413128111  0.458
2014 Shen QT, Schuh AL, Zheng Y, Quinney K, Wang L, Hanna M, Mitchell JC, Otegui MS, Ahlquist P, Cui Q, Audhya A. Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly. The Journal of Cell Biology. 206: 763-77. PMID 25202029 DOI: 10.1083/Jcb.201403108  0.315
2014 Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, ... ... Mitchell JC, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439  0.443
2013 Zhu X, Ericksen SS, Demerdash ON, Mitchell JC. Data-driven models for protein interaction and design. Proteins. 81: 2221-8. PMID 24038640 DOI: 10.1002/Prot.24405  0.766
2013 Pattnaik BR, Tokarz S, Asuma MP, Schroeder T, Sharma A, Mitchell JC, Edwards AO, Pillers DA. Snowflake vitreoretinal degeneration (SVD) mutation R162W provides new insights into Kir7.1 ion channel structure and function. Plos One. 8: e71744. PMID 23977131 DOI: 10.1371/Journal.Pone.0071744  0.324
2013 Zhu X, Ericksen SS, Mitchell JC. DBSI: DNA-binding site identifier. Nucleic Acids Research. 41: e160. PMID 23873960 DOI: 10.1093/Nar/Gkt617  0.464
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Mitchell JC, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  0.752
2013 Demerdash ON, Mitchell JC. Using physical potentials and learned models to distinguish native binding interfaces from de novo designed interfaces that do not bind. Proteins. 81: 1919-30. PMID 23760773 DOI: 10.1002/Prot.24337  0.775
2012 Demerdash ON, Mitchell JC. Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis. Proteins. 80: 1766-79. PMID 22434479 DOI: 10.1002/Prot.24072  0.704
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031  0.749
2011 Zhu X, Mitchell JC. KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features. Proteins. 79: 2671-83. PMID 21735484 DOI: 10.1002/Prot.23094  0.449
2010 Demerdash ON, Buyan A, Mitchell JC. ReplicOpter: a replicate optimizer for flexible docking. Proteins. 78: 3156-65. PMID 20715288 DOI: 10.1002/Prot.22811  0.756
2009 Demerdash ON, Daily MD, Mitchell JC. Structure-based predictive models for allosteric hot spots. Plos Computational Biology. 5: e1000531. PMID 19816556 DOI: 10.1371/Journal.Pcbi.1000531  0.75
2008 Bannen RM, Suresh V, Phillips GN, Wright SJ, Mitchell JC. Optimal design of thermally stable proteins. Bioinformatics (Oxford, England). 24: 2339-43. PMID 18723523 DOI: 10.1093/Bioinformatics/Btn450  0.337
2008 Darnell SJ, LeGault L, Mitchell JC. KFC Server: interactive forecasting of protein interaction hot spots. Nucleic Acids Research. 36: W265-9. PMID 18539611 DOI: 10.1093/Nar/Gkn346  0.767
2007 Darnell SJ, Page D, Mitchell JC. An automated decision-tree approach to predicting protein interaction hot spots. Proteins. 68: 813-23. PMID 17554779 DOI: 10.1002/Prot.21474  0.763
2007 Marcia RF, Mitchell JC, Wright SJ. Global optimization in protein docking using clustering, underestimation and semidefinite programming Optimization Methods and Software. 22: 803-811. DOI: 10.1080/00207170701203756  0.357
2007 Marcia RF, Mitchell JC, Rosen JB. Multi-funnel optimization using Gaussian underestimation Journal of Global Optimization. 39: 39-48. DOI: 10.1007/S10898-006-9110-4  0.351
2006 Kedlaya RH, Bhat KM, Mitchell J, Darnell SJ, Setaluri V. TRP1 interacting PDZ-domain protein GIPC forms oligomers and is localized to intracellular vesicles in human melanocytes. Archives of Biochemistry and Biophysics. 454: 160-9. PMID 16962991 DOI: 10.1016/J.Abb.2006.08.010  0.739
2005 Rutkoski TJ, Kurten EL, Mitchell JC, Raines RT. Disruption of shape-complementarity markers to create cytotoxic variants of ribonuclease A. Journal of Molecular Biology. 354: 41-54. PMID 16188273 DOI: 10.1016/J.Jmb.2005.08.007  0.361
2005 Marcia RF, Mitchell JC, Rosen JB. Iterative convex quadratic approximation for global optimization in protein docking Computational Optimization and Applications. 32: 285-297. DOI: 10.1007/S10589-005-4799-4  0.337
2004 Zbilut JP, Giuliani A, Colosimo A, Mitchell JC, Colafranceschi M, Marwan N, Webber CL, Uversky VN. Charge and hydrophobicity patterning along the sequence predicts the folding mechanism and aggregation of proteins: a computational approach. Journal of Proteome Research. 3: 1243-53. PMID 15595734 DOI: 10.1021/Pr049883+  0.415
2004 Mitchell JC, Shahbaz S, Ten Eyck LF. Interfaces in Molecular Docking Molecular Simulation. 30: 97-106. DOI: 10.1080/0892702031000152217  0.373
2004 Zbilut JP, Mitchell JC, Giuliani A, Colosimo A, Marwan N, Webber CL. Singular hydrophobicity patterns and net charge: A mesoscopic principle for protein aggregation/folding Physica a: Statistical Mechanics and Its Applications. 343: 348-358. DOI: 10.1016/J.Physa.2004.05.081  0.368
2003 Law DS, Ten Eyck LF, Katzenelson O, Tsigelny I, Roberts VA, Pique ME, Mitchell JC. Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information. Proteins. 52: 33-40. PMID 12784365 DOI: 10.1002/Prot.10395  0.36
2001 Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, Tsigelny I, Ten Eyck LF. Protein docking using continuum electrostatics and geometric fit. Protein Engineering. 14: 105-13. PMID 11297668 DOI: 10.1093/Protein/14.2.105  0.356
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