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 …
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 …
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 …
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 …
Motivation: Structural prediction of protein interactions currently remains a challenging but fundamental goal. In particular, progress in scoring functions is critical for the efficient …
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 …
Motivation Knowledge-based statistical potentials constitute a simpler and easier alternative to physics-based potentials in many applications, including folding, docking and protein …
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 …
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 …