Principles and overview of sampling methods for modeling macromolecular structure and dynamics

T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

[PDF][PDF] The folding of single domain proteins-have we reached a consensus?

TR Sosnick - Biophysical Journal, 2011 - cell.com
The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. This talk will provide
an overview of new approaches to study and manipulate signaling in living cells and …

Protein 3D structure computed from evolutionary sequence variation

DS Marks, LJ Colwell, R Sheridan, TA Hopf, A Pagnani… - PloS one, 2011 - journals.plos.org
The evolutionary trajectory of a protein through sequence space is constrained by its
function. Collections of sequence homologs record the outcomes of millions of evolutionary …

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Y Yang, J Gao, J Wang, R Heffernan… - Briefings in …, 2018 - academic.oup.com
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted
helical and sheet conformations for protein polypeptide backbone even before the first …

Elucidation of amyloid β-protein oligomerization mechanisms: discrete molecular dynamics study

B Urbanc, M Betnel, L Cruz, G Bitan… - Journal of the American …, 2010 - ACS Publications
Oligomers of amyloid β-protein (Aβ) play a central role in the pathology of Alzheimer's
disease. Of the two predominant Aβ alloforms, Aβ1− 40 and Aβ1− 42, Aβ1− 42 is more …

The molecular basis for modulation of human Vγ9Vδ2 T cell responses by CD277/butyrophilin-3 (BTN3A)-specific antibodies

A Palakodeti, A Sandstrom, L Sundaresan… - Journal of Biological …, 2012 - ASBMB
Human Vγ9Vδ2 T cells are well known for their rapid and potent response to infection and
tumorigenesis when in the presence of endogenous or exogenous phosphoisoprenoids …

Protein 8-class secondary structure prediction using conditional neural fields

Z Wang, F Zhao, J Peng, J Xu - 2010 IEEE International …, 2010 - ieeexplore.ieee.org
Compared to the protein 3-class secondary structure (SS) prediction, the 8-class prediction
gains less attention and is also much more challenging, especially for proteins with few …

[HTML][HTML] Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction

E Faraggi, Y Yang, S Zhang, Y Zhou - Structure, 2009 - cell.com
Local structures predicted from protein sequences are used extensively in every aspect of
modeling and prediction of protein structure and function. For more than 50 years, they have …

Basin hopping as a general and versatile optimization framework for the characterization of biological macromolecules

B Olson, I Hashmi, K Molloy… - Advances in Artificial …, 2012 - Wiley Online Library
Since its introduction, the basin hopping (BH) framework has proven useful for hard
nonlinear optimization problems with multiple variables and modalities. Applications span a …

The 2.5 Å structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation

L Scharf, NS Li, AJ Hawk, D Garzón, T Zhang, LM Fox… - Immunity, 2010 - cell.com
CD1 molecules function to present lipid-based antigens to T cells. Here we present the
crystal structure of CD1c at 2.5 Å resolution, in complex with the pathogenic Mycobacterium …