Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank
H Wako, S Endo - Biophysical reviews, 2017 - Springer
Normal mode analysis (NMA) can facilitate quick and systematic investigation of protein
dynamics using data from the Protein Data Bank (PDB). We developed an elastic network …
dynamics using data from the Protein Data Bank (PDB). We developed an elastic network …
Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy
Single-particle analysis by electron microscopy is a well established technique for analyzing
the three-dimensional structures of biological macromolecules. Besides its ability to produce …
the three-dimensional structures of biological macromolecules. Besides its ability to produce …
Protein elastic network models and the ranges of cooperativity
Elastic network models (ENMs) are entropic models that have demonstrated in many
previous studies their abilities to capture overall the important internal motions, with …
previous studies their abilities to capture overall the important internal motions, with …
Computational and experimental characterization of RNA cubic nanoscaffolds
KA Afonin, W Kasprzak, E Bindewald… - Therapeutic RNA …, 2021 - taylorfrancis.com
122The fast-developing 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 …
Prediction of methionine oxidation risk in monoclonal antibodies using a machine learning method
Monoclonal antibodies (mAbs) have become a major class of protein therapeutics that target
a spectrum of diseases ranging from cancers to infectious diseases. Similar to any protein …
a spectrum of diseases ranging from cancers to infectious diseases. Similar to any protein …
Molecular dynamics simulation of triclinic lysozyme in a crystal lattice
PA Janowski, C Liu, J Deckman, DA Case - Protein science, 2016 - Wiley Online Library
Molecular dynamics simulations of crystals can enlighten interpretation of experimental X‐
ray crystallography data and elucidate structural dynamics and heterogeneity in …
ray crystallography data and elucidate structural dynamics and heterogeneity in …
The systematic modeling studies and free energy calculations of the phenazine compounds as anti-tuberculosis agents
Y Wang, A Khan, A Chandra Kaushik… - Journal of …, 2019 - Taylor & Francis
Phenazine compounds have good activity against Mycobacterium tuberculosis (MTB).
Based on the reported activities that were obtained in MTB H37Rv, a three-dimensional …
Based on the reported activities that were obtained in MTB H37Rv, a three-dimensional …
Parameterizing elastic network models to capture the dynamics of proteins
Coarse‐grained normal mode analyses of protein dynamics rely on the idea that the
geometry of a protein structure contains enough information for computing its fluctuations …
geometry of a protein structure contains enough information for computing its fluctuations …
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 …
Could Dermaseptin analogue be a competitive inhibitor for ACE2 towards binding with viral spike protein causing COVID19?: computational investigation
PC Sekar, R Rajasekaran - International Journal of Peptide Research and …, 2021 - Springer
Initial phase of COVID-19 infection is associated with the binding of viral spike protein S1
receptor binding domain (RBD) with the host cell surface receptor, ACE2. Peptide inhibitors …
receptor binding domain (RBD) with the host cell surface receptor, ACE2. Peptide inhibitors …