Kueppers F., Andrake M.D., Xu Q., Dunbrack R.L., Jr., Kim J., Sanders C.L., Protein modeling to assess the pathogenicity of rare variants of serpina1 in patients suspected of having alpha 1 antitrypsin deficiency. BMC Med Genet. 20(1): 125, 2019. PMC6631921. 1.740
Modi V., Dunbrack R.L., Jr., A structurally-validated multiple sequence alignment of 497 human protein kinase domains. Sci Rep. 9(1): 19790, 2019. PMC6930252. 4.011
Modi V., Dunbrack R.L., Jr., Defining a new nomenclature for the structures of active and inactive kinases. Proc Natl Acad Sci U S A. 116(14): 6818-6827, 2019. PMC6452665. 9.580
Nicolas E., Demidova E.V., Iqbal W., Serebriiskii I.G., Vlasenkova R., Ghatalia P., Zhou Y., Rainey K., Forman A.F., Dunbrack R.L., Jr., Golemis E.A., Hall M.J., Daly M.B., Arora S., Interaction of germline variants in a family with a history of early-onset clear cell renal cell carcinoma. Mol Genet Genomic Med. 7(3): e556, 2019. PMC6418363. 9.924
Shapovalov M., Vucetic S., Dunbrack R.L., Jr., A new clustering and nomenclature for beta turns derived from high-resolution protein structures. PLoS Comput Biol. 15(3): e1006844, 2019. PMC6424458. 4.428
Xu Q., Dunbrack R.L., Jr., Principles and characteristics of biological assemblies in experimentally determined protein structures. Curr Opin Struct Biol. 55: 34-49, 2019. 7.052
Adolf-Bryfogle J, Kalyuzhniy O, Kubitz M, Weitzner BD, Hu X, Adachi Y, Schief WR, Dunbrack RL, Jr. RosettaAntibodyDesign (RAbD): A general framework for computational antibody design. PLoS computational biology, 14(4):e1006112, 2018. PMC5942852
Fahl SP, Coffey F, Kain L, Zarin P, Dunbrack RL, Jr., Teyton L, Zuniga-Pflucker JC, Kappes DJ, Wiest DL. Role of a selecting ligand in shaping the murine gammadelta-TCR repertoire. Proceedings of the National Academy of Sciences of the United States of America, 115(8):1889-94, 2018. PMC5828614
Matthew EM, Yang Z, Peri S, Andrake M, Dunbrack R, Ross E, El-Deiry WS. Plk2 Loss Commonly Occurs in Colorectal Carcinomas but not Adenomas: Relationship to mTOR Signaling. Neoplasia (New York, NY), 20(3):244-55, 2018. PMC5849802
Fahl SP, Coffey F, Kain L, Zarin P, Dunbrack RL, Jr., Teyton L, Zuniga-Pflucker JC, Kappes DJ, Wiest DL. Role of a selecting ligand in shaping the murine gammadelta-TCR repertoire. Proc Natl Acad Sci U S A, 115(8):1889-94, 2018. PMC5828614
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. Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4. Hum Mutat, 38(9):1123-31, 2017. PMC5561472
Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL Jr, Gray JJ. Modeling and docking of antibodies with Rosetta. Nature Protocols 12:401-416, 2017. PMCID: in process.
Huwe PJ, Xu Q, Shapovalov MV, Modi V Andrake MD, Dunbrack RL. Biological function derived from predicted structures in CASP11. Proteins 84 Suppl. 1:370-391, 2016. DOI: 10.1002/prot.24997; PMCID: PMC4963311.
Adolf-Bryfogle J, Xu Q, North B, Lehmann A, Dunbrack RL Jr. PyIgClassify: A database of antibody CDR structural classifications. Nucleic Acids Research (database issue) 43:D432-438, 2015. DOI: 10.1093/nar/gku1106; PMCID: PMC4383924.
Lehmann AK, Wixted JHF, Shapovalov MV, Roder H, Dunbrack RL Jr.,* Robinson MK.* Stability engineering of anti-EGFR scFv antibodies by rational design of a -to- swap of the VL framework using a structure-guided approach. mAbs 7:1058-1071, 2015. DOI:10.1080/19420862.2015.1088618; PMCID: PMC4966335. ... Expand
Weitzner BD, Dunbrack RL Jr.,* Gray JJ*. The origin of CDR H3 structural diversity. Structure 23:302-311, 2015. *Corresponding authors. PMCID: PMC4318709.
Xu Q, Malecka KL, Fink L, Jordan JJ, Duffy E, Kolander S, Peterson J, Dunbrack RL Jr. Three-dimensional structures of autophosphorylation complexes in crystals of protein kinases. Science Signaling 8:rs13, 2015. DOI:10.1126/scisignal.aaa6711; PMCID: PMC4766099.
Shapovalov MV, Wang Q, Xu Q, Andrake MD, Dunbrack RL Jr. BioAssemblyModeler (BAM): User-friendly homology modeling of protein homo- and heterooligomers. PLOS ONE 9:e98309, 2014. PMCID: PMC4055448.
Wei Q, Dunbrack RL Jr. The role of balanced training and testing data sets for binary classifiers in bioinformatics. PLOS ONE 8:e67863, 2013. PMCID: PMC3706434.
Wei Q, Xu Q, Dunbrack RL Jr. Prediction of phenotypes of missense mutations in human proteins from the structures of biological assemblies. Proteins 81:199-213, 2013. PMCID: PMC3552143.
Berkholz DS, Driggers CM, Shapovalov MV, Dunbrack RL Jr., Karplus PA. Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc Natl Acad Sci USA 109:449-453, 2012. PMCID: PMC3258596.