[HTML][HTML] In silico methods for design of biological therapeutics
It has been twenty years since the first rationally designed small molecule drug was
introduced into the market. Since then, we have progressed from designing small molecules …
introduced into the market. Since then, we have progressed from designing small molecules …
Incorporation of solvent effect into multi-objective evolutionary algorithm for improved protein structure prediction
The problem of predicting the three-dimensional (3-D) structure of a protein from its one-
dimensional sequence has been called the “holy grail of molecular biology”, and it has …
dimensional sequence has been called the “holy grail of molecular biology”, and it has …
[HTML][HTML] Analysis of biostructural changes, dynamics, and interactions–small-angle X-ray scattering to the rescue
B Vestergaard - Archives of biochemistry and biophysics, 2016 - Elsevier
Solution small angle X-ray scattering from biological macromolecules (BioSAXS) plays an
increasingly important role in biostructural research. The analysis of complex protein …
increasingly important role in biostructural research. The analysis of complex protein …
Bayesian inference of protein ensembles from SAXS data
The inherent flexibility of intrinsically disordered proteins (IDPs) and multi-domain proteins
with intrinsically disordered regions (IDRs) presents challenges to structural analysis. These …
with intrinsically disordered regions (IDRs) presents challenges to structural analysis. These …
Inference of structure ensembles of flexible biomolecules from sparse, averaged data
We present the theoretical foundations of a general principle to infer structure ensembles of
flexible biomolecules from spatially and temporally averaged data obtained in biophysical …
flexible biomolecules from spatially and temporally averaged data obtained in biophysical …
Molecular dynamics simulations of human FOXO3 reveal intrinsically disordered regions spread spatially by intramolecular electrostatic repulsion
ROJ Weinzierl - Biomolecules, 2021 - mdpi.com
The human transcription factor FOXO3 (a member of the 'forkhead'family of transcription
factors) controls a variety of cellular functions that make it a highly relevant target for …
factors) controls a variety of cellular functions that make it a highly relevant target for …
New horizons in structural biology of membrane proteins: experimental evaluation of the role of conformational dynamics and intrinsic flexibility
R Puthenveetil, ET Christenson, O Vinogradova - Membranes, 2022 - mdpi.com
A plethora of membrane proteins are found along the cell surface and on the convoluted
labyrinth of membranes surrounding organelles. Since the advent of various structural …
labyrinth of membranes surrounding organelles. Since the advent of various structural …
Structural phylogenetics with confidence
For evaluating the deepest evolutionary relationships among proteins, sequence similarity is
too low for application of sequence-based homology search or phylogenetic methods. In …
too low for application of sequence-based homology search or phylogenetic methods. In …
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering
MJ Bakker, A Gaffour, M Juhás, V Zapletal… - Journal of Chemical …, 2024 - ACS Publications
By merging advanced dimensionality reduction (DR) and clustering algorithm (CA)
techniques, our study advances the sampling procedure for predicting NMR chemical shifts …
techniques, our study advances the sampling procedure for predicting NMR chemical shifts …
Probabilistic determination of native state ensembles of proteins
The motions of biological macromolecules are tightly coupled to their functions. However,
while the study of fast motions has become increasingly feasible in recent years, the study of …
while the study of fast motions has become increasingly feasible in recent years, the study of …