Results 31 to 40 of about 45,576 (293)

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Biochemistry, 2021
Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design.
Clara T. Schoeder, S. Schmitz, Jared Adolf-Bryfogle, A. M. Sevy, J. A. Finn, Marion Sauer, N. Bozhanova, Benjamin K. Mueller, Amandeep K. Sangha, J. Bonet, J. Sheehan, G. Kuenze, Brennica Marlow, Shannon T. Smith, Hope Woods, B. Bender, Cristina E. Martina, Diego del Alamo, Pranav Kodali, Alican Gulsevin, W. Schief, B. Correia, J. Crowe, J. Meiler, Rocco Moretti   +24 more
semanticscholar   +1 more source

microRNA‐122 as a regulator of mitochondrial metabolic gene network in hepatocellular carcinoma

Molecular Systems Biology, 2010
Tumorigenesis involves multistep genetic alterations. To elucidate the microRNA (miRNA)–gene interaction network in carcinogenesis, we examined their genome‐wide expression profiles in 96 pairs of tumor/non‐tumor tissues from hepatocellular carcinoma ...
Julja Burchard, Chunsheng Zhang, Angela M Liu, Ronnie T P Poon, Nikki P Y Lee, Kwong‐Fai Wong, Pak C Sham, Brian Y Lam, Mark D Ferguson, George Tokiwa, Ryan Smith, Brendan Leeson, Rebecca Beard, John R Lamb, Lee Lim, Mao Mao, Hongyue Dai, John M Luk   +17 more
doaj   +1 more source

Thematic review series: Systems Biology Approaches to Metabolic and Cardiovascular Disorders. Reverse engineering gene networks to identify key drivers of complex disease phenotypes

Journal of Lipid Research, 2006
Diseases such as obesity, diabetes, and atherosclerosis result from multiple genetic and environmental factors, and importantly, interactions between genetic and environmental factors. Identifying susceptibility genes for these diseases using genetic and
Eric E. Schadt, Pek Y. Lum
doaj   +1 more source

PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes

bioRxiv, 2020
Proteolysis-targeting chimeras (PROTACs), which induce degradation by recruitment of an E3 ligase to a target protein, are gaining much interest as a new pharmacological modality. However, designing PROTACs is challenging.
D. Zaidman, N. London
semanticscholar   +1 more source

Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design. [PDF]

PLoS ONE, 2012
Noncanonical amino acids (NCAAs) can be used in a variety of protein design contexts. For example, they can be used in place of the canonical amino acids (CAAs) to improve the biophysical properties of peptides that target protein interfaces. We describe
P Douglas Renfrew, Eun Jung Choi, Richard Bonneau, Brian Kuhlman   +3 more
doaj   +1 more source

Construction and Characterization of T7 Bacteriophages Harboring Apidaecin-Derived Sequences

Current Issues in Molecular Biology, 2022
The global spread of multi- and pan-resistant bacteria has triggered research to identify novel strategies to fight these pathogens, such as antimicrobial peptides and, more recently, bacteriophages.
Tobias Ludwig, Ralf Hoffmann, Andor Krizsan   +2 more
doaj   +1 more source

Chromosome 20q Amplification Regulates Response to Kinesin-5 Inhibitor

Cancer Informatics, 2008
We identified gene expression signatures predicting responsiveness to a Kinesin-5 (KIF11) inhibitor (Kinesin-5i) in cultured colon tumor cell lines.
Aimee L. Jackson, Mao Mao, Sumire Kobayashi, Teresa Ward, Matthew Biery, Hongyue Dai, Steven R. Bartz, Peter S. Linsley   +7 more
doaj   +1 more source

Real-time PyMOL visualization for Rosetta and PyRosetta. [PDF]

PLoS ONE, 2011
Computational structure prediction and design of proteins and protein-protein complexes have long been inaccessible to those not directly involved in the field.
Evan H Baugh, Sergey Lyskov, Brian D Weitzner, Jeffrey J Gray   +3 more
doaj   +1 more source

Rationalizing PROTAC-mediated Ternary Complex Formation using Rosetta

bioRxiv, 2020
PROTACs are molecules that combine a target-binding warhead with an E3 ligase-recruiting moiety; by drawing the target protein into a ternary complex with the E3 ligase, PROTACs induce target protein degradation.
N. Bai, P. Kirubakaran, J. Karanicolas
semanticscholar   +1 more source

Cometary Chemistry and the Origin of Icy Solar System Bodies: The View After Rosetta [PDF]

Annual Review of Astronomy and Astrophysics, 2019
In situ research of cometary chemistry began when measurements from the Giotto mission at Comet 1P/Halley revealed the presence of complex organics in the coma.
K. Altwegg, H. Balsiger, S. Fuselier
semanticscholar   +1 more source