IBBR Publications

Burns LA, Faver JC, Zheng Z, Marshall MS, Smith DGA, Vanommeslaeghe K, Mackerell AD, Merz KM, C Sherrill D. The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions. J Chem Phys. 2017 ;147(16):161727.

Karageorgos I, Gallagher ES, Galvin C, D Gallagher T, Hudgens JW. Biophysical characterization and structure of the Fab fragment from the NIST reference antibody, RM 8671. Biologicals. 2017 .

Pal LR, Kundu K, Yin Y, Moult J. CAGI4 Crohn's exome challenge: Marker SNP versus exome variant models for assigning risk of Crohn disease. Hum Mutat. 2017 .

Pal LR, Kundu K, Yin Y, Moult J. CAGI4 SickKids clinical genomes challenge: A pipeline for identifying pathogenic variants. Hum Mutat. 2017 .

Zang F, Gerasopoulos K, Brown AD, Culver JN, Ghodssi R. Capillary microfluidics-assembled virus-like particle bio-nano-receptor interfaces for label-free biosensing. ACS Appl Mater Interfaces. 2017 .

Quigley J, V Hughitt K, Velikovsky CA, Mariuzza RA, El-Sayed NM, Briken V. The Cell Wall Lipid PDIM Contributes to Phagosomal Escape and Host Cell Exit of Mycobacterium tuberculosis. MBio. 2017 ;8(2).

Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, Mackerell AD. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat Methods. 2017 ;14(1):71-73.

Jo S, Cheng X, Lee J, Kim S, Park S-J, Patel DS, Beaven AH, Lee KIl, Rui H, Park S, et al. CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem. 2017 ;38(15):1114-1124.

Kim J, Sinha S, Solomon M, Perez-Herrero E, Hsu J, Tsinas Z, Muro S. Co-coating of receptor-targeted drug nanocarriers with anti-phagocytic moieties enhances specific tissue uptake versus non-specific phagocytic clearance. Biomaterials. 2017 ;147:14-25.

Gao S, Linden SB, Nelson DC. Complete Genome Sequence of Klebsiella pneumoniae Phages SopranoGao, MezzoGao, and AltoGao. Genome Announc. 2017 ;5(45).

Yu W, Mackerell AD. Computer-Aided Drug Design Methods. Methods Mol Biol. 2017 ;1520:85-106.

Mazur SJ, Gallagher ES, Debnath S, Durell SR, Anderson KW, Jenkins LMMiller, Appella E, Hudgens JW. Conformational Changes in Active and Inactive States of Human PP2Cα Characterized by Hydrogen/Deuterium Exchange-Mass Spectrometry. Biochemistry [Internet]. 2017 . Available from: http://pubs.acs.org/doi/abs/10.1021/acs.biochem.6b01220

Yang M, Huang J, Simon R, Wang L-X, Mackerell AD. Conformational Heterogeneity of the HIV Envelope Glycan Shield. Sci Rep. 2017 ;7(1):4435.

Yang M, Simon R, Mackerell AD. Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155-4. J Phys Chem B. 2017 ;121(15):3412-3423.

Liu Y, Li J, Tschirhart T, Terrell JL, Kim E, Tsao C-Y, Kelly DL, Bentley WE, Payne GF. Connecting Biology to Electronics: Molecular Communication via Redox Modality. Adv Healthc Mater. 2017 .

Mckay R, Hauk P, Wu H-C, Pottash AEli, Shang W, Terrell J, Payne GF, Bentley WE. Controlling Localization of E. coli Populations Using a Two-Part Synthetic Motility Circuit: An Accelerator and Brake. Biotechnol Bioeng. 2017 .

Wu H-C, Quan DN, Tsao C-Y, Liu Y, Terrell JL, Luo X, Yang J-C, Payne GF, Bentley WE. Cover Image, Volume 114, Number 1, January 2017. Biotechnol Bioeng. 2017 ;114(1):i.

Häcker I, Harrell RA, Eichner G, Pilitt KL, O'Brochta DA, Handler AM, Schetelig MF. Cre/lox-Recombinase-Mediated Cassette Exchange for Reversible Site-Specific Genomic Targeting of the Disease Vector, Aedes aegypti. Sci Rep. 2017 ;7:43883.

Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical Assessment of Methods of Protein Structure Prediction (CASP) - Round XII. Proteins. 2017 .

Pidugu LSwarna Muk, Neu H, Wong TLok, Pozharski E, Molloy JL, Michel SLJ, Toth EA. Crystal structures of human 3-hydroxyanthranilate 3,4-dioxygenase with native and non-native metals bound in the active site. Acta Crystallogr D Struct Biol. 2017 ;73(Pt 4):340-348.

Mast N, Anderson KW, Lin JB, Li Y, Turko IV, Tatsuoka C, Bjorkhem I, Pikuleva IA. Cytochrome P450 27A1 Deficiency and Regional Differences in Brain Sterol Metabolism Cause Preferential Cholestanol Accumulation in the Cerebellum. J Biol Chem. 2017 .

Fuerst TR, Pierce BG, Keck Z-Y, Foung SKH. Designing a B Cell-Based Vaccine against a Highly Variable Hepatitis C Virus. Front Microbiol. 2017 ;8:2692.

Kundu K, Pal LR, Yin Y, Moult J. Determination of disease phenotypes and pathogenic variants from exome sequence data in the CAGI 4 gene panel challenge. Hum Mutat. 2017 .

Baliban SM, Yang M, Ramachandran G, Curtis B, Shridhar S, Laufer RS, Wang JY, Van Druff J, Higginson EE, Hegerle N, et al. Development of a glycoconjugate vaccine to prevent invasive Salmonella Typhimurium infections in sub-Saharan Africa. PLoS Negl Trop Dis. 2017 ;11(4):e0005493.

Kelman LM, Kelman Z. Do Archaea Need an Origin of Replication?. Trends Microbiol. 2017 .