Computational amide I 2D IR spectroscopy as a probe of protein structure and dynamics

M Reppert, A Tokmakoff - Annual Review of Physical Chemistry, 2016 - annualreviews.org
Two-dimensional infrared spectroscopy of amide I vibrations is increasingly being used to
study the structure and dynamics of proteins and peptides. Amide I, a primarily carbonyl …

A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction

J Zhang, Y Zhang - PloS one, 2010 - journals.plos.org
Background An accurate potential function is essential to attack protein folding and structure
prediction problems. The key to developing efficient knowledge-based potential functions is …

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 …

OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing

M Lu, AD Dousis, J Ma - Journal of molecular biology, 2008 - Elsevier
Here we report an orientation-dependent statistical all-atom potential derived from side-
chain packing, named OPUS-PSP. It features a basis set of 19 rigid-body blocks extracted …

How well can the accuracy of comparative protein structure models be predicted?

D Eramian, N Eswar, MY Shen, A Sali - Protein Science, 2008 - Wiley Online Library
Comparative structure models are available for two orders of magnitude more protein
sequences than are experimentally determined structures. These models, however, suffer …

InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution

J Andreani, G Faure, R Guerois - Bioinformatics, 2013 - academic.oup.com
Motivation: Structural prediction of protein interactions currently remains a challenging but
fundamental goal. In particular, progress in scoring functions is critical for the efficient …

New statistical potential for quality assessment of protein models and a survey of energy functions

D Rykunov, A Fiser - BMC bioinformatics, 2010 - Springer
Background Scoring functions, such as molecular mechanic forcefields and statistical
potentials are fundamentally important tools in protein structure modeling and quality …

KORP: knowledge-based 6D potential for fast protein and loop modeling

JR López-Blanco, P Chacón - Bioinformatics, 2019 - academic.oup.com
Motivation Knowledge-based statistical potentials constitute a simpler and easier alternative
to physics-based potentials in many applications, including folding, docking and protein …

Mimicking the folding pathway to improve homology-free protein structure prediction

J DeBartolo, A Colubri, AK Jha… - Proceedings of the …, 2009 - National Acad Sciences
Since the demonstration that the sequence of a protein encodes its structure, the prediction
of structure from sequence remains an outstanding problem that impacts numerous scientific …

Explicit orientation dependence in empirical potentials and its significance to side-chain modeling

J Ma - Accounts of chemical research, 2009 - ACS Publications
Protein structure modeling and prediction have important applications throughout the
biological sciences, from the design of pharmaceuticals to the elucidation of enzyme …