Integrating molecular simulation and experimental data: a Bayesian/maximum entropy reweighting approach

S Bottaro, T Bengtsen, K Lindorff-Larsen - … bioinformatics: methods and …, 2020 - Springer
Abstract We describe a Bayesian/Maximum entropy (BME) procedure and software to
construct a conformational ensemble of a biomolecular system by integrating molecular …

Hybrid approaches to structural characterization of conformational ensembles of complex macromolecular systems combining NMR residual dipolar couplings and …

V Venditti, TK Egner, GM Clore - Chemical reviews, 2016 - ACS Publications
Solving structures or structural ensembles of large macromolecular systems in solution
poses a challenging problem. While NMR provides structural information at atomic …

Role of water in protein folding, oligomerization, amyloidosis and miniprotein

T Vajda, A Perczel - Journal of Peptide Science, 2014 - Wiley Online Library
The essential involvement of water in most fundamental extra‐cellular and intracellular
processes of proteins is critically reviewed and evaluated in this article. The role of water in …

Integrated NMR, fluorescence, and molecular dynamics benchmark study of protein mechanics and hydrodynamics

C Möckel, J Kubiak, O Schillinger… - The Journal of …, 2018 - ACS Publications
Understanding the function of a protein requires not only knowledge of its tertiary structure
but also an understanding of its conformational dynamics. Nuclear magnetic resonance …

[图书][B] Structural Bioinformatics

Z Gáspári - 2020 - Springer
Structural biology is built on the axiom that understanding biomolecular processes in detail
requires explicit knowledge of the atomic-level structure of the macromolecules involved …

The exact NOE as an alternative in ensemble structure determination

B Vögeli, S Olsson, P Güntert, R Riek - Biophysical journal, 2016 - cell.com
The structure-function paradigm is increasingly replaced by the structure-dynamics-function
paradigm. All protein activity is steered by the interplay between enthalpy and entropy …

Active site breathing of human Alkbh5 revealed by solution NMR and accelerated molecular dynamics

JA Purslow, TT Nguyen, TK Egner, RR Dotas… - Biophysical …, 2018 - cell.com
Abstract AlkB homolog 5 (Alkbh5) is one of nine members of the AlkB family, which are
nonheme Fe 2+/α-ketoglutarate-dependent dioxygenases that catalyze the oxidative …

Overview update: computational prediction of intrinsic disorder in proteins

VN Uversky, L Kurgan - Current Protocols, 2023 - Wiley Online Library
There are over 100 computational predictors of intrinsic disorder. These methods predict
amino acid‐level propensities for disorder directly from protein sequences. The propensities …

Solution Structure Ensembles of the Open and Closed Forms of the∼ 130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and NMR

SL Sedinkin, D Burns, D Shukla… - Journal of the …, 2023 - ACS Publications
Large-scale interdomain rearrangements are essential to protein function, governing the
activity of large enzymes and molecular machineries. Yet, obtaining an atomic-resolution …

Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs

E Papaleo, C Camilloni, K Teilum, M Vendruscolo… - PeerJ, 2018 - peerj.com
Many proteins display complex dynamical properties that are often intimately linked to their
biological functions. As the native state of a protein is best described as an ensemble of …