Quantitative approaches for decoding the specificity of the human T cell repertoire
T cell receptor (TCR)-peptide-major histocompatibility complex (pMHC) interactions play a
vital role in initiating immune responses against pathogens, and the specificity of TCRpMHC …
vital role in initiating immune responses against pathogens, and the specificity of TCRpMHC …
Birth and future of multiscale modeling for macromolecular systems (Nobel Lecture)
M Levitt - Angewandte Chemie International Edition, 2014 - Wiley Online Library
Winning the Nobel Prize is a unique and marvelous experience that no one can prepare for
or in any way know what to expect. The instantaneous transformation from an ordinary …
or in any way know what to expect. The instantaneous transformation from an ordinary …
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction
RNA molecules play fundamental roles in cellular processes. Their function and interactions
with other biomolecules are dependent on the ability to form complex three-dimensional …
with other biomolecules are dependent on the ability to form complex three-dimensional …
Avoiding false positive conclusions in molecular simulation: the importance of replicas
Molecular simulations are a computational technique used to investigate the dynamics of
proteins and other molecules. The free energy landscape of these simulations is often …
proteins and other molecules. The free energy landscape of these simulations is often …
A nucleotide-level coarse-grained model of RNA
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining
methodology recently developed for the oxDNA model of DNA. The model is designed to …
methodology recently developed for the oxDNA model of DNA. The model is designed to …
Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis
Abstract Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific
ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we …
ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we …
Modeling nucleic acids
Nucleic acids are an important class of biological macromolecules that carry out a variety of
cellular roles. For many functions, naturally occurring DNA and RNA molecules need to fold …
cellular roles. For many functions, naturally occurring DNA and RNA molecules need to fold …
[HTML][HTML] Coarse-grained modeling of RNA 3D structure
Functional RNA molecules depend on three-dimensional (3D) structures to carry out their
tasks within the cell. Understanding how these molecules interact to carry out their biological …
tasks within the cell. Understanding how these molecules interact to carry out their biological …
A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect
YZ Shi, FH Wang, YY Wu, ZJ Tan - The Journal of chemical physics, 2014 - pubs.aip.org
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs,
some computational models have been proposed for predicting RNA 3D structures …
some computational models have been proposed for predicting RNA 3D structures …
Computational and experimental characterization of RNA cubic nanoscaffolds
122The fast-develo** field of RNA nanotechnology requires the adoption and
development of novel and faster computational approaches to modeling and …
development of novel and faster computational approaches to modeling and …