Third generation antibody discovery methods: in silico rational design
Owing to their outstanding performances in molecular recognition, antibodies are
extensively used in research and applications in molecular biology, biotechnology and …
extensively used in research and applications in molecular biology, biotechnology and …
Advances in coarse-grained modeling of macromolecular complexes
Highlights•Coarse-grained models are reduced representations of all-atom models that aim
to retain the essential molecular aspects for the system of interest.•Coarse-grained …
to retain the essential molecular aspects for the system of interest.•Coarse-grained …
Toward reliable and insightful entropy calculations on flexible molecules
N Díaz, D Suárez - Journal of Chemical Theory and Computation, 2022 - ACS Publications
The absolute entropy of a flexible molecule can be approximated by the sum of a rigid-rotor-
harmonic-oscillator (RRHO) entropy and a Gibbs–Shannon entropy associated to the …
harmonic-oscillator (RRHO) entropy and a Gibbs–Shannon entropy associated to the …
Peptide mediated antimicrobial dental adhesive system
The most common cause for dental composite failures is secondary caries due to invasive
bacterial colonization of the adhesive/dentin (a/d) interface. Innate material weakness often …
bacterial colonization of the adhesive/dentin (a/d) interface. Innate material weakness often …
Entropy of proteins using multiscale cell correlation
A Chakravorty, J Higham… - Journal of Chemical …, 2020 - ACS Publications
A new multiscale method is presented to calculate the entropy of proteins from molecular
dynamics simulations. Termed Multiscale Cell Correlation (MCC), the method decomposes …
dynamics simulations. Termed Multiscale Cell Correlation (MCC), the method decomposes …
Characterizing and predicting protein hinges for mechanistic insight
The functioning of proteins requires highly specific dynamics, which depend critically on the
details of how amino acids are packed. Hinge motions are the most common type of large …
details of how amino acids are packed. Hinge motions are the most common type of large …
Comparisons of protein dynamics from experimental structure ensembles, molecular dynamics ensembles, and coarse-grained elastic network models
Predicting protein motions is important for bridging the gap between protein structure and
function. With growing numbers of structures of the same or closely related proteins …
function. With growing numbers of structures of the same or closely related proteins …
Entropies derived from the packing geometries within a single protein structure
PM Khade, RL Jernigan - ACS omega, 2022 - ACS Publications
A fast, simple, yet robust method to calculate protein entropy from a single protein structure
is presented here. The focus is on the atomic packing details, which are calculated by …
is presented here. The focus is on the atomic packing details, which are calculated by …
An aromatic amino acid and associated helix in the C-terminus of the potato leafroll virus minor capsid protein regulate systemic infection and symptom expression
Y Xu, WL Da Silva, Y Qian, SM Gray - PLoS Pathogens, 2018 - journals.plos.org
The C-terminal region of the minor structural protein of potato leafroll virus (PLRV), known as
the readthrough protein (RTP), is involved in efficient virus movement, tissue tropism and …
the readthrough protein (RTP), is involved in efficient virus movement, tissue tropism and …
Directional force originating from ATP hydrolysis drives the GroEL conformational change
Protein functional mechanisms usually require conformational changes, and often there are
known structures for the different conformational states. However, usually neither the origin …
known structures for the different conformational states. However, usually neither the origin …