The protein folding problem

KA Dill, SB Ozkan, MS Shell, TR Weikl - Annu. Rev. Biophys., 2008 - annualreviews.org
The “protein folding problem” consists of three closely related puzzles:(a) What is the folding
code?(b) What is the folding mechanism?(c) Can we predict the native structure of a protein …

[HTML][HTML] Recent advances in developing web-servers for predicting protein attributes

KC Chou, HB Shen - Natural science, 2009 - scirp.org
Recent advance in large-scale genome se-quencing has generated a huge volume of pro-
tein sequences. In order to timely utilize the in-formation hidden in these newly discovered …

Radius of gyration as an indicator of protein structure compactness

MY Lobanov, NS Bogatyreva, OV Galzitskaya - Molecular Biology, 2008 - Springer
Identification and study of the main principles underlying the kinetics and thermodynamics of
protein folding generate a new insight into the factors that control this process. Statistical …

Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naive Bayes

W Lou, X Wang, F Chen, Y Chen, B Jiang, H Zhang - PloS one, 2014 - journals.plos.org
Developing an efficient method for determination of the DNA-binding proteins, due to their
vital roles in gene regulation, is becoming highly desired since it would be invaluable to …

Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet

E Shakhnovich - Chemical reviews, 2006 - ACS Publications
As was noted in our recent review, 1 the protein folding field underwent a cyclic
development. Initially, protein folding was viewed as a strictly experimental field belonging to …

RNA and protein folding: common themes and variations

D Thirumalai, C Hyeon - Biochemistry, 2005 - ACS Publications
Visualizing the navigation of an ensemble of unfolded molecules through the bumpy energy
landscape in search of the native state gives a pictorial view of biomolecular folding. This …

Chaperonin mechanisms: Multiple and (mis) understood?

A Horovitz, TH Reingewertz, J Cuéllar… - Annual review of …, 2022 - annualreviews.org
The chaperonins are ubiquitous and essential nanomachines that assist in protein folding in
an ATP-driven manner. They consist of two back-to-back stacked oligomeric rings with …

Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models

HS Chan, Z Zhang, S Wallin, Z Liu - Annual review of physical …, 2011 - annualreviews.org
Coarse-grained, self-contained polymer models are powerful tools in the study of protein
folding. They are also essential to assess predictions from less rigorous theoretical …

How well can simulation predict protein folding kinetics and thermodynamics?

CD Snow, EJ Sorin, YM Rhee… - Annu. Rev. Biophys …, 2005 - annualreviews.org
▪ Abstract Simulation of protein folding has come a long way in five years. Notably, new
quantitative comparisons with experiments for small, rapidly folding proteins have become …

Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions

P Limpikirati, T Liu, RW Vachet - Methods, 2018 - Elsevier
Using mass spectrometry (MS) to obtain information about a higher order structure of protein
requires that a protein's structural properties are encoded into the mass of that protein …