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Items: 1 to 50 of 113

1.

Principles and characteristics of biological assemblies in experimentally determined protein structures.

Xu Q, Dunbrack RL Jr.

Curr Opin Struct Biol. 2019 Apr 6;55:34-49. doi: 10.1016/j.sbi.2019.03.006. [Epub ahead of print] Review.

PMID:
30965224
2.

Defining a new nomenclature for the structures of active and inactive kinases.

Modi V, Dunbrack RL Jr.

Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):6818-6827. doi: 10.1073/pnas.1814279116. Epub 2019 Mar 13.

3.

A new clustering and nomenclature for beta turns derived from high-resolution protein structures.

Shapovalov M, Vucetic S, Dunbrack RL Jr.

PLoS Comput Biol. 2019 Mar 7;15(3):e1006844. doi: 10.1371/journal.pcbi.1006844. eCollection 2019 Mar.

4.

Interaction of germline variants in a family with a history of early-onset clear cell renal cell carcinoma.

Nicolas E, Demidova EV, Iqbal W, Serebriiskii IG, Vlasenkova R, Ghatalia P, Zhou Y, Rainey K, Forman AF, Dunbrack RL Jr, Golemis EA, Hall MJ, Daly MB, Arora S.

Mol Genet Genomic Med. 2019 Mar;7(3):e556. doi: 10.1002/mgg3.556. Epub 2019 Jan 24.

5.

Mouse modeling and structural analysis of the p.G307S mutation in human cystathionine β-synthase (CBS) reveal effects on CBS activity but not stability.

Gupta S, Kelow S, Wang L, Andrake MD, Dunbrack RL Jr, Kruger WD.

J Biol Chem. 2018 Sep 7;293(36):13921-13931. doi: 10.1074/jbc.RA118.002164. Epub 2018 Jul 20.

PMID:
30030379
6.

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design.

Adolf-Bryfogle J, Kalyuzhniy O, Kubitz M, Weitzner BD, Hu X, Adachi Y, Schief WR, Dunbrack RL Jr.

PLoS Comput Biol. 2018 Apr 27;14(4):e1006112. doi: 10.1371/journal.pcbi.1006112. eCollection 2018 Apr.

7.

Role of a selecting ligand in shaping the murine γδ-TCR repertoire.

Fahl SP, Coffey F, Kain L, Zarin P, Dunbrack RL Jr, Teyton L, Zúñiga-Pflücker JC, Kappes DJ, Wiest DL.

Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):1889-1894. doi: 10.1073/pnas.1718328115. Epub 2018 Feb 5.

8.

BRCA2, EGFR, and NTRK mutations in mismatch repair-deficient colorectal cancers with MSH2 or MLH1 mutations.

Deihimi S, Lev A, Slifker M, Shagisultanova E, Xu Q, Jung K, Vijayvergia N, Ross EA, Xiu J, Swensen J, Gatalica Z, Andrake M, Dunbrack RL, El-Deiry WS.

Oncotarget. 2017 Jun 20;8(25):39945-39962. doi: 10.18632/oncotarget.18098.

9.

Functional analysis of rare variants in mismatch repair proteins augments results from computation-based predictive methods.

Arora S, Huwe PJ, Sikder R, Shah M, Browne AJ, Lesh R, Nicolas E, Deshpande S, Hall MJ, Dunbrack RL Jr, Golemis EA.

Cancer Biol Ther. 2017 Jul 3;18(7):519-533. doi: 10.1080/15384047.2017.1326439. Epub 2017 May 11.

10.

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL Jr, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ.

J Chem Theory Comput. 2017 Jun 13;13(6):3031-3048. doi: 10.1021/acs.jctc.7b00125. Epub 2017 May 12.

11.

Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4.

Xu Q, Tang Q, Katsonis P, Lichtarge O, Jones D, Bovo S, Babbi G, Martelli PL, Casadio R, Lee GR, Seok C, Fenton AW, Dunbrack RL Jr.

Hum Mutat. 2017 Sep;38(9):1123-1131. doi: 10.1002/humu.23222. Epub 2017 May 2.

12.

Modeling and docking of antibody structures with Rosetta.

Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL Jr, Gray JJ.

Nat Protoc. 2017 Feb;12(2):401-416. doi: 10.1038/nprot.2016.180. Epub 2017 Jan 26.

13.

Biological function derived from predicted structures in CASP11.

Huwe PJ, Xu Q, Shapovalov MV, Modi V, Andrake MD, Dunbrack RL Jr.

Proteins. 2016 Sep;84 Suppl 1:370-91. doi: 10.1002/prot.24997. Epub 2016 Jun 15.

14.

Assessment of template-based modeling of protein structure in CASP11.

Modi V, Xu Q, Adhikari S, Dunbrack RL Jr.

Proteins. 2016 Sep;84 Suppl 1:200-20. doi: 10.1002/prot.25049. Epub 2016 Jun 15.

15.

Assessment of refinement of template-based models in CASP11.

Modi V, Dunbrack RL Jr.

Proteins. 2016 Sep;84 Suppl 1:260-81. doi: 10.1002/prot.25048. Epub 2016 Jun 15.

16.

CASP 11 target classification.

Kinch LN, Li W, Schaeffer RD, Dunbrack RL, Monastyrskyy B, Kryshtafovych A, Grishin NV.

Proteins. 2016 Sep;84 Suppl 1:20-33. doi: 10.1002/prot.24982. Epub 2016 Jan 27.

17.

Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases.

Xu Q, Malecka KL, Fink L, Jordan EJ, Duffy E, Kolander S, Peterson JR, Dunbrack RL Jr.

Sci Signal. 2015 Dec 1;8(405):rs13. doi: 10.1126/scisignal.aaa6711.

18.

Systematic evaluation of underlying defects in DNA repair as an approach to case-only assessment of familial prostate cancer.

Nicolas E, Arora S, Zhou Y, Serebriiskii IG, Andrake MD, Handorf ED, Bodian DL, Vockley JG, Dunbrack RL, Ross EA, Egleston BL, Hall MJ, Golemis EA, Giri VN, Daly MB.

Oncotarget. 2015 Nov 24;6(37):39614-33. doi: 10.18632/oncotarget.5554.

19.

Stability engineering of anti-EGFR scFv antibodies by rational design of a lambda-to-kappa swap of the VL framework using a structure-guided approach.

Lehmann A, Wixted JH, Shapovalov MV, Roder H, Dunbrack RL Jr, Robinson MK.

MAbs. 2015;7(6):1058-71. doi: 10.1080/19420862.2015.1088618. Epub 2015 Sep 4.

20.

Cancer Signature Investigation: ERBB2 (HER2)-Activating Mutation and Amplification-Positive Breast Carcinoma Mimicking Lung Primary.

Shih J, Bashir B, Gustafson KS, Andrake M, Dunbrack RL, Goldstein LJ, Boumber Y.

J Natl Compr Canc Netw. 2015 Aug;13(8):947-52.

21.

Defects in DNA Repair Genes Predict Response to Neoadjuvant Cisplatin-based Chemotherapy in Muscle-invasive Bladder Cancer.

Plimack ER, Dunbrack RL, Brennan TA, Andrake MD, Zhou Y, Serebriiskii IG, Slifker M, Alpaugh K, Dulaimi E, Palma N, Hoffman-Censits J, Bilusic M, Wong YN, Kutikov A, Viterbo R, Greenberg RE, Chen DY, Lallas CD, Trabulsi EJ, Yelensky R, McConkey DJ, Miller VA, Golemis EA, Ross EA.

Eur Urol. 2015 Dec;68(6):959-67. doi: 10.1016/j.eururo.2015.07.009. Epub 2015 Aug 1.

22.

Characteristics of clinical trials that require participants to be fluent in English.

Egleston BL, Pedraza O, Wong YN, Dunbrack RL Jr, Griffin CL, Ross EA, Beck JR.

Clin Trials. 2015 Dec;12(6):618-26. doi: 10.1177/1740774515592881. Epub 2015 Jul 7.

23.

The origin of CDR H3 structural diversity.

Weitzner BD, Dunbrack RL Jr, Gray JJ.

Structure. 2015 Feb 3;23(2):302-11. doi: 10.1016/j.str.2014.11.010. Epub 2015 Jan 8.

24.

Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors.

Vijayan RS, He P, Modi V, Duong-Ly KC, Ma H, Peterson JR, Dunbrack RL Jr, Levy RM.

J Med Chem. 2015 Jan 8;58(1):466-79. doi: 10.1021/jm501603h. Epub 2014 Dec 12.

25.

PyIgClassify: a database of antibody CDR structural classifications.

Adolf-Bryfogle J, Xu Q, North B, Lehmann A, Dunbrack RL Jr.

Nucleic Acids Res. 2015 Jan;43(Database issue):D432-8. doi: 10.1093/nar/gku1106. Epub 2014 Nov 11.

26.

Issues in interpreting the in vivo activity of Aurora-A.

Shagisultanova E, Dunbrack RL Jr, Golemis EA.

Expert Opin Ther Targets. 2015 Feb;19(2):187-200. doi: 10.1517/14728222.2014.981154. Epub 2014 Nov 11. Review.

27.

BioAssemblyModeler (BAM): user-friendly homology modeling of protein homo- and heterooligomers.

Shapovalov MV, Wang Q, Xu Q, Andrake M, Dunbrack RL Jr.

PLoS One. 2014 Jun 12;9(6):e98309. doi: 10.1371/journal.pone.0098309. eCollection 2014.

28.

Acetylation of the transcriptional repressor Ume6p allows efficient promoter release and timely induction of the meiotic transient transcription program in yeast.

Law MJ, Mallory MJ, Dunbrack RL Jr, Strich R.

Mol Cell Biol. 2014 Feb;34(4):631-42. doi: 10.1128/MCB.00256-13. Epub 2013 Dec 2.

29.

A highly selective dual insulin receptor (IR)/insulin-like growth factor 1 receptor (IGF-1R) inhibitor derived from an extracellular signal-regulated kinase (ERK) inhibitor.

Anastassiadis T, Duong-Ly KC, Deacon SW, Lafontant A, Ma H, Devarajan K, Dunbrack RL Jr, Wu J, Peterson JR.

J Biol Chem. 2013 Sep 27;288(39):28068-77. doi: 10.1074/jbc.M113.505032. Epub 2013 Aug 9.

30.

The role of balanced training and testing data sets for binary classifiers in bioinformatics.

Wei Q, Dunbrack RL Jr.

PLoS One. 2013 Jul 9;8(7):e67863. doi: 10.1371/journal.pone.0067863. Print 2013.

31.

The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite.

Adolf-Bryfogle J, Dunbrack RL Jr.

PLoS One. 2013 Jul 9;8(7):e66856. doi: 10.1371/journal.pone.0066856. Print 2013.

32.

Charge asymmetry in the proteins of the outer membrane.

Slusky JS, Dunbrack RL Jr.

Bioinformatics. 2013 Sep 1;29(17):2122-8. doi: 10.1093/bioinformatics/btt355. Epub 2013 Jun 19.

33.

Architecture and assembly of HIV integrase multimers in the absence of DNA substrates.

Bojja RS, Andrake MD, Merkel G, Weigand S, Dunbrack RL Jr, Skalka AM.

J Biol Chem. 2013 Mar 8;288(10):7373-86. doi: 10.1074/jbc.M112.434431. Epub 2013 Jan 14.

34.

A modified HSP70 inhibitor shows broad activity as an anticancer agent.

Balaburski GM, Leu JI, Beeharry N, Hayik S, Andrake MD, Zhang G, Herlyn M, Villanueva J, Dunbrack RL Jr, Yen T, George DL, Murphy ME.

Mol Cancer Res. 2013 Mar;11(3):219-29. doi: 10.1158/1541-7786.MCR-12-0547-T. Epub 2013 Jan 9.

35.

A new model for allosteric regulation of phenylalanine hydroxylase: implications for disease and therapeutics.

Jaffe EK, Stith L, Lawrence SH, Andrake M, Dunbrack RL Jr.

Arch Biochem Biophys. 2013 Feb 15;530(2):73-82. doi: 10.1016/j.abb.2012.12.017. Epub 2013 Jan 11.

36.

Prediction of phenotypes of missense mutations in human proteins from biological assemblies.

Wei Q, Xu Q, Dunbrack RL Jr.

Proteins. 2013 Feb;81(2):199-213. doi: 10.1002/prot.24176. Epub 2012 Nov 5.

37.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.

Xu Q, Dunbrack RL Jr.

Bioinformatics. 2012 Nov 1;28(21):2763-72. doi: 10.1093/bioinformatics/bts533. Epub 2012 Aug 31.

38.

Aurora A kinase (AURKA) in normal and pathological cell division.

Nikonova AS, Astsaturov I, Serebriiskii IG, Dunbrack RL Jr, Golemis EA.

Cell Mol Life Sci. 2013 Feb;70(4):661-87. doi: 10.1007/s00018-012-1073-7. Epub 2012 Aug 3. Review.

39.

CD45-deficient severe combined immunodeficiency caused by uniparental disomy.

Roberts JL, Buckley RH, Luo B, Pei J, Lapidus A, Peri S, Wei Q, Shin J, Parrott RE, Dunbrack RL Jr, Testa JR, Zhong XP, Wiest DL.

Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10456-61. doi: 10.1073/pnas.1202249109. Epub 2012 Jun 11.

40.

Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites.

Berkholz DS, Driggers CM, Shapovalov MV, Dunbrack RL Jr, Karplus PA.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):449-53. doi: 10.1073/pnas.1107115108. Epub 2011 Dec 23.

41.

Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization.

Krieger E, Dunbrack RL Jr, Hooft RW, Krieger B.

Methods Mol Biol. 2012;819:405-21. doi: 10.1007/978-1-61779-465-0_25.

PMID:
22183550
42.

Minimal ensembles of side chain conformers for modeling protein-protein interactions.

Beglov D, Hall DR, Brenke R, Shapovalov MV, Dunbrack RL Jr, Kozakov D, Vajda S.

Proteins. 2012 Feb;80(2):591-601. doi: 10.1002/prot.23222. Epub 2011 Nov 22.

43.

Protein-intrinsic and signaling network-based sources of resistance to EGFR- and ErbB family-targeted therapies in head and neck cancer.

Mehra R, Serebriiskii IG, Dunbrack RL Jr, Robinson MK, Burtness B, Golemis EA.

Drug Resist Updat. 2011 Dec;14(6):260-79. doi: 10.1016/j.drup.2011.08.002. Epub 2011 Sep 14. Review.

44.

A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions.

Shapovalov MV, Dunbrack RL Jr.

Structure. 2011 Jun 8;19(6):844-58. doi: 10.1016/j.str.2011.03.019.

45.

The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms.

Xu Q, Dunbrack RL Jr.

Nucleic Acids Res. 2011 Jan;39(Database issue):D761-70. doi: 10.1093/nar/gkq1059. Epub 2010 Oct 29.

46.

A new clustering of antibody CDR loop conformations.

North B, Lehmann A, Dunbrack RL Jr.

J Mol Biol. 2011 Feb 18;406(2):228-56. doi: 10.1016/j.jmb.2010.10.030. Epub 2010 Oct 28.

47.

Rapid calcium-dependent activation of Aurora-A kinase.

Plotnikova OV, Pugacheva EN, Dunbrack RL, Golemis EA.

Nat Commun. 2010 Sep 7;1:64. doi: 10.1038/ncomms1061.

48.

Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation.

Doulias PT, Greene JL, Greco TM, Tenopoulou M, Seeholzer SH, Dunbrack RL, Ischiropoulos H.

Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16958-63. doi: 10.1073/pnas.1008036107. Epub 2010 Sep 13.

49.

Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase.

Wei Q, Wang L, Wang Q, Kruger WD, Dunbrack RL Jr.

Proteins. 2010 Jul;78(9):2058-74. doi: 10.1002/prot.22722.

50.

Development of a rotamer library for use in beta-peptide foldamer computational design.

Shandler SJ, Shapovalov MV, Dunbrack RL Jr, DeGrado WF.

J Am Chem Soc. 2010 Jun 2;132(21):7312-20. doi: 10.1021/ja906700x.

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