Energy density functions for protein structures

N Thamwattana, JA Mccoy, JM Hill - The Quarterly Journal of …, 2008 - academic.oup.com
In this paper, we adopt the calculus of variations to study the structure of protein with an
energy functional dependent on the curvature, torsion and their derivatives with respect to …

Processing of as-48ABC RNA in AS-48 Enterocin Production by Enterococcus faecalis

M Fernández, M Sánchez-Hidalgo… - Journal of …, 2008 - Am Soc Microbiol
Enterocin AS-48 production and immunity characters are encoded by 10 genes (as-
48ABCC1DD1EFGH) of the pMB2 plasmid from the Enterococcus faecalis S-48 strain …

All-atom level direct folding simulation of a ββα miniprotein

S Jang, E Kim, Y Pak - The Journal of chemical physics, 2008 - pubs.aip.org
We performed ab initio folding simulation for a β β α peptide BBA5 (PDB code 1T8J) with a
modified param99 force field using the generalized Born solvation model …

[图书][B] Optimization in medicine and biology

GJ Lim, EK Lee - 2008 - taylorfrancis.com
Thanks to recent advancements, optimization is now recognized as a crucial component in
research and decision-making across a number of fields. Through optimization, scientists …

fRMSDPred: Predicting local RMSD between structural fragments using sequence information

H Rangwala, G Karypis - Proteins: Structure, Function, and …, 2008 - Wiley Online Library
The effectiveness of comparative modeling approaches for protein structure prediction can
be substantially improved by incorporating predicted structural information in the initial …

[HTML][HTML] Benchmarking of TASSER_2. 0: an improved protein structure prediction algorithm with more accurate predicted contact restraints

SY Lee, J Skolnick - Biophysical Journal, 2008 - cell.com
To improve tertiary structure predictions of more difficult targets, the next generation of
TASSER, TASSER_2. 0, has been developed. TASSER_2. 0 incorporates more accurate …

Conformational landscape of the HIV-V3 hairpin loop from all-atom free-energy simulations

A Verma, W Wenzel - The Journal of chemical physics, 2008 - pubs.aip.org
Small beta hairpins have many distinct biological functions, including their involvement in
chemokine and viral receptor recognition. The relevance of structural similarities between …

Protein folding and beyond: Energy landscapes and the organization of living matter in time and space

PG Wolynes - Physical Biology: From Atoms to Medicine, 2008 - World Scientific
Proteins are highly dynamical entities. The folding, function and higher order assembly of
biomacromolecules are key elements of the organization of living matter. Energy landscape …

Structural Bioinformatics: Transforming protein structures into biological insights

Y Kalidas, N Chandra - Journal of the Indian Institute of Science, 2008 - journal.iisc.ac.in
Structural bioinformatics is an area that has emerged to comprehend and interpret large
amounts of structural data, and promises to provide a high resolution understanding of …

[图书][B] New protein structure prediction method using inter-residue distances and a theoretical investigation of the isomerization of azobenzene and disubstituted …

CR Crecca - 2008 - search.proquest.com
It is often claimed that knowing a protein's structure is important in understanding its function.
The experimental structure determination methods presently available can be costly and …