Biomolecular modeling and simulation: a field coming of age

T Schlick, R Collepardo-Guevara… - Quarterly reviews of …, 2011 - cambridge.org
We assess the progress in biomolecular modeling and simulation, focusing on structure
prediction and dynamics, by presenting the field's history, metrics for its rise in popularity …

Protein flexibility and ligand recognition: challenges for molecular modeling

F Spyrakis, A BidonChanal, X Barril… - Current topics in …, 2011 - ingentaconnect.com
The intrinsic dynamics of macromolecules is an essential property to relate the structure of
biomolecular systems with their function in the cell. In the field of ligand-receptor recognition …

Micellization studied by GPU-accelerated coarse-grained molecular dynamics

BG Levine, DN LeBard, R DeVane… - Journal of Chemical …, 2011 - ACS Publications
The computational design of advanced materials based on surfactant self-assembly without
ever stepping foot in the laboratory is an important goal, but there are significant barriers to …

Randomized tree construction algorithm to explore energy landscapes

L Jaillet, FJ Corcho, JJ Pérez… - Journal of computational …, 2011 - Wiley Online Library
In this work, a new method for exploring conformational energy landscapes is described.
The method, called transition‐rapidly exploring random tree (T‐RRT), combines ideas from …

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 …

High temperatures enhance cooperative motions between CBM and catalytic domains of a thermostable cellulase: mechanism insights from essential dynamics

PR Batista, MG de Souza Costa, PG Pascutti… - Physical Chemistry …, 2011 - pubs.rsc.org
Cellulases from thermophiles are capable of cleaving sugar chains from cellulose efficiently
at high temperatures. The thermo-resistant Cel9A-68 cellulase possesses two important …

[PDF][PDF] Use of Metadynamics in the Design of isoDGR-Based avb3 Antagonists To Fine-Tune the Conformational Ensemble

A Spitaleri, M Ghitti, S Mari, L Alberici… - Angew. Chem. Int …, 2011 - academia.edu
The integrin family of cell-adhesion receptors regulates cellular functions crucial to the
initiation, progression, and metastasis of solid tumors. In particular, integrin αvβ3 plays a key …

Effect of using suboptimal alignments in template‐based protein structure prediction

H Chen, D Kihara - Proteins: Structure, Function, and …, 2011 - Wiley Online Library
Computational protein structure prediction remains a challenging task in protein
bioinformatics. In the recent years, the importance of template‐based structure prediction is …

Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent

A Rodriguez, P Mokoema, F Corcho… - The Journal of …, 2011 - ACS Publications
The prediction capabilities of atomistic simulations of peptides are hampered by different
difficulties, including the reliability of force fields, the treatment of the solvent or the adequate …

Conformational diseases: structural studies of aggregation of polyglutamine proteins

E Papaleo, G Invernizzi - Current computer-aided drug design, 2011 - ingentaconnect.com
Protein misfolding and aggregation into insoluble amyloid deposits are often associated with
neurodegenerative disorders. In particular, the polyglutamine (polyQ) diseases are inherited …