Computational techniques for efficient conformational sampling of proteins

A Liwo, C Czaplewski, S Ołdziej… - Current opinion in …, 2008‏ - Elsevier
In this review, we summarize the computational methods for sampling the conformational
space of biomacromolecules. We discuss the methods applicable to find only lowest energy …

Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads

Y Bai, M Ni, B Cooper, Y Wei, W Fury - BMC genomics, 2014‏ - Springer
Background Accurate HLA ty** at amino acid level (four-digit resolution) is critical in
hematopoietic and organ transplantations, pathogenesis studies of autoimmune and …

Trends in template/fragment-free protein structure prediction

Y Zhou, Y Duan, Y Yang, E Faraggi, H Lei - Theoretical chemistry accounts, 2011‏ - Springer
Predicting the structure of a protein from its amino acid sequence is a long-standing
unsolved problem in computational biology. Its solution would be of both fundamental and …

Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps

A Bitran, WM Jacobs, X Zhai, E Shakhnovich - Proceedings of the National …, 2020‏ - pnas.org
Many large proteins suffer from slow or inefficient folding in vitro. It has long been known that
this problem can be alleviated in vivo if proteins start folding cotranslationally. However, the …

All-atom ab initio folding of a diverse set of proteins

JS Yang, WW Chen, J Skolnick, EI Shakhnovich - Structure, 2007‏ - cell.com
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding
process and prediction of the native fold of proteins are two major unsolved problems in …

Universality and diversity of folding mechanics for three-helix bundle proteins

JS Yang, S Wallin, EI Shakhnovich - … of the National Academy of Sciences, 2008‏ - pnas.org
In this study we evaluate, at full atomic detail, the folding processes of two small helical
proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by …

Interdisciplinary applied mathematics

SSAJE Marsden, LSS Wiggins, L Glass, RV Kohn… - 1993‏ - Springer
Problems in engineering, computational science, and the physical and biological sciences
are using increasingly sophisticated mathematical techniques. Thus, the bridge between the …

Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics

F Wang, SJ Stuart, RA Latour - Biointerphases, 2008‏ - pubs.aip.org
The adsorption behavior of a biomolecule, such as a peptide or protein, to a functionalized
surface is of fundamental importance for a broad range of applications in biotechnology. The …

LOCUSTRA: accurate prediction of local protein structure using a two-layer support vector machine approach

O Zimmermann, UHE Hansmann - Journal of chemical information …, 2008‏ - ACS Publications
Constraint generation for 3d structure prediction and structure-based database searches
benefit from fine-grained prediction of local structure. In this work, we present LOCUSTRA, a …

Modelling proteins: Conformational sampling and reconstruction of folding kinetics

K Klenin, B Strodel, DJ Wales, W Wenzel - Biochimica et Biophysica Acta …, 2011‏ - Elsevier
In the last decades biomolecular simulation has made tremendous inroads to help elucidate
biomolecular processes in-silico. Despite enormous advances in molecular dynamics …