Guide for determination of protein structural ensembles by combining cryo-EM data with metadynamics.
Sign Up to like & getrecommendations! Published in 2022 at "FEBS open bio"
DOI: 10.1002/2211-5463.13542
Abstract: Metadynamics Electron Microscopy MetaInference (MEMMI) is an integrative structural biology method that enables a rapid and accurate characterization of protein structural dynamics at the atomic level and the error in the Cryo-EM experimental data, even… read more here.
Keywords: structural ensembles; microscopy; cryo; protein structural ... See more keywords
Prediction of protein structural class based on symmetrical recurrence quantification analysis
Sign Up to like & getrecommendations! Published in 2021 at "Computational biology and chemistry"
DOI: 10.1016/j.compbiolchem.2021.107450
Abstract: Protein structural class prediction for low similarity sequences is a significant challenge and one of the deeply explored subjects. This plays an important role in drug design, folding recognition of protein, functional analysis and several… read more here.
Keywords: analysis; protein structural; biology; structural class ... See more keywords
Protein structural motifs in prediction and design.
Sign Up to like & getrecommendations! Published in 2017 at "Current opinion in structural biology"
DOI: 10.1016/j.sbi.2017.03.012
Abstract: The Protein Data Bank (PDB) has been an integral resource for shaping our fundamental understanding of protein structure and for the advancement of such applications as protein design and structure prediction. Over the years, information… read more here.
Keywords: motifs prediction; structural motifs; protein structural; biology ... See more keywords
Unraveling protein's structural dynamics: from configurational dynamics to ensemble switching guides functional mesoscale assemblies.
Sign Up to like & getrecommendations! Published in 2020 at "Current opinion in structural biology"
DOI: 10.1016/j.sbi.2020.10.016
Abstract: Evidence regarding protein structure and function manifest the imperative role that dynamics play in proteins, underlining reconsideration of the unanimated sequence-to-structure-to-function paradigm. Structural dynamics portray a heterogeneous energy landscape described by conformational ensembles where each… read more here.
Keywords: mesoscale assemblies; protein structural; structural dynamics; unraveling protein ... See more keywords
Protein Structural Denaturation Evaluated by MCR-ALS of Protein Microarray FTIR Spectra.
Sign Up to like & getrecommendations! Published in 2021 at "Analytical chemistry"
DOI: 10.1021/acs.analchem.1c01416
Abstract: The loss of native structure is common in proteins. Among others, aggregation is one structural modification of particular importance as it is a major concern for the efficiency and safety of biotherapeutic proteins. Yet, recognizing… read more here.
Keywords: protein; denaturation evaluated; protein structural; mcr als ... See more keywords
Mapping Protein Structural Evolution upon Unfolding.
Sign Up to like & getrecommendations! Published in 2022 at "Biochemistry"
DOI: 10.1021/acs.biochem.1c00743
Abstract: In the past, many intensive attempts failed to capture or underestimated the copopulated intermediate conformers from the protein folding/unfolding reaction. We report a promising approach to kinetically trap, resolve, and quantify protein conformers that evolve… read more here.
Keywords: upon unfolding; mapping protein; protein structural; structural evolution ... See more keywords
X-ray Scattering Studies of Protein Structural Dynamics.
Sign Up to like & getrecommendations! Published in 2017 at "Chemical reviews"
DOI: 10.1021/acs.chemrev.6b00790
Abstract: X-ray scattering is uniquely suited to the study of disordered systems and thus has the potential to provide insight into dynamic processes where diffraction methods fail. In particular, while X-ray crystallography has been a staple… read more here.
Keywords: protein structural; structural dynamics; studies protein; ray scattering ... See more keywords
Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry
Sign Up to like & getrecommendations! Published in 2017 at "Nature Protocols"
DOI: 10.1038/nprot.2017.100
Abstract: Protein structural changes induced by external perturbations or internal cues can profoundly influence protein activity and thus modulate cellular physiology. A number of biophysical approaches are available to probe protein structural changes, but these are… read more here.
Keywords: structural changes; mass spectrometry; proteolysis coupled; protein structural ... See more keywords
Banking on protein structural data
Sign Up to like & getrecommendations! Published in 2021 at "Science"
DOI: 10.1126/science.abl8151
Abstract: In 1953, the proposed structure of DNA magnificently linked biological function and structure. By contrast, 4 years later, the first elucidation of the structure of a protein—myoglobin, by Kendrew and colleagues—revealed an inelegant shape, described… read more here.
Keywords: banking protein; protein structural; structural data; structure ... See more keywords
Prediction of protein structural classes by different feature expressions based on 2-D wavelet denoising and fusion
Sign Up to like & getrecommendations! Published in 2019 at "BMC Bioinformatics"
DOI: 10.1186/s12859-019-3276-5
Abstract: Protein structural class predicting is a heavily researched subject in bioinformatics that plays a vital role in protein functional analysis, protein folding recognition, rational drug design and other related fields. However, when traditional feature expression… read more here.
Keywords: feature; protein structural; wavelet denoising; structural classes ... See more keywords
Development of a TSR-Based Method for Protein 3-D Structural Comparison With Its Applications to Protein Classification and Motif Discovery
Sign Up to like & getrecommendations! Published in 2020 at "Frontiers in Chemistry"
DOI: 10.3389/fchem.2020.602291
Abstract: Development of protein 3-D structural comparison methods is important in understanding protein functions. At the same time, developing such a method is very challenging. In the last 40 years, ever since the development of the… read more here.
Keywords: protein structural; method; structure; structural comparison ... See more keywords