[HTML][HTML] Hybrid methods for combined experimental and computational determination of protein structure

JT Seffernick, S Lindert - The Journal of chemical physics, 2020 - pubs.aip.org
Knowledge of protein structure is paramount to the understanding of biological function,
developing new therapeutics, and making detailed mechanistic hypotheses. Therefore …

Computational modeling of membrane proteins

J Koehler Leman, MB Ulmschneider… - … Structure, Function, and …, 2015 - Wiley Online Library
The determination of membrane protein (MP) structures has always trailed that of soluble
proteins due to difficulties in their overexpression, reconstitution into membrane mimetics …

Development of a prototype system for archiving integrative/hybrid structure models of biological macromolecules

B Vallat, B Webb, JD Westbrook, A Sali, HM Berman - Structure, 2018 - cell.com
Essential processes in biology are carried out by large macromolecular assemblies, whose
structures are often difficult to determine by traditional methods. Increasingly, researchers …

Federating structural models and data: outcomes from a workshop on archiving integrative structures

HM Berman, PD Adams, AA Bonvin, SK Burley… - Structure, 2019 - cell.com
Structures of biomolecular systems are increasingly computed by integrative modeling. In
this approach, a structural model is constructed by combining information from multiple …

A glance into the evolution of template-free protein structure prediction methodologies

S Dhingra, R Sowdhamini, F Cadet, B Offmann - Biochimie, 2020 - Elsevier
Prediction of protein structures using computational approaches has been explored for over
two decades, paving a way for more focused research and development of algorithms in …

Finding the needle in the haystack: towards solving the protein-folding problem computationally

B Li, M Fooksa, S Heinze, J Meiler - Critical reviews in biochemistry …, 2018 - Taylor & Francis
Prediction of protein tertiary structures from amino acid sequence and understanding the
mechanisms of how proteins fold, collectively known as “the protein folding problem,” has …

Protein structure prediction guided by crosslinking restraints–A systematic evaluation of the impact of the crosslinking spacer length

T Hofmann, AW Fischer, J Meiler, S Kalkhof - Methods, 2015 - Elsevier
Recent development of high-resolution mass spectrometry (MS) instruments enables
chemical crosslinking (XL) to become a high-throughput method for obtaining structural …

Prediction of protein complex structure using surface-induced dissociation and cryo-electron microscopy

JT Seffernick, SM Canfield, SR Harvey… - Analytical …, 2021 - ACS Publications
A variety of techniques involving the use of mass spectrometry (MS) have been developed to
obtain structural information on proteins and protein complexes. One example of these …

Rapid simulation of unprocessed DEER decay data for protein fold prediction

D Del Alamo, MH Tessmer, RA Stein, JB Feix… - Biophysical …, 2020 - cell.com
Despite advances in sampling and scoring strategies, Monte Carlo modeling methods still
struggle to accurately predict de novo the structures of large proteins, membrane proteins, or …

Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints

G Kuenze, R Bonneau, JK Leman, J Meiler - Structure, 2019 - cell.com
Computational methods to predict protein structure from nuclear magnetic resonance (NMR)
restraints that only require assignment of backbone signals, hold great potential to study …