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Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle
Crystal structures group II chaperonin reveal closed states associated protein folding cycle
2015/12/11
Chaperonins are large protein complexes consisting of two stacked multisubunit rings, which open and close in an ATP-dependent manner to create a protected environment for protein folding. Here, we de...
First principles structures and circular dichroism spectra for the close-packed and the 7/2 motif of collagen
First principles structures circular dichroism spectra the 7/2 motif of collagen Biological Physics
2012/5/17
The recently proposed close-packed motif for collagen is investigated using first principles semi-empirical wave function theory and Kohn-Sham density functional theory. Under these refinements the cl...
Computational Potential Energy Minimization Studies on the Prion AGAAAAGA Amyloid Fibril Molecular Structures
Computational Potential Energy Minimization Amyloid Fibril Molecular Structures Biological Physics
2012/5/3
X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, and dual polarization interferometry, etc are indeed very powerful tools to determine the 3D structures of proteins (including the...
Realistic 3D computer model of the gerbil middle ear, featuring accurate morphology of bone and soft tissue structures
gerbil, middle ear, modeling, high-resolution, three-dimensional, soft tissue, surface mesh,micro-scale X-ray computed tomography (micro-CT), orthogonal-plane fluorescence optical-sectioning microscopy (OPFOS)
2011/9/14
In order to improve realism in middle ear (ME) finite element modeling (FEM), comprehensive and precise morphological data are needed. To date, micro-scale X-ray computed tomography (μCT) recordings ...
Atomic-resolution structures of prion AGAAAAGA amyloid fibrils
Amyloid Fibrils Prion AGAAAAGA Palindrome Atomic-resolution Structures
2011/8/31
To the best of the authors knowledge, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins due to the unstable, noncrystalline and...
Cooperative hierarchical structures emerging in multiadaptive games
Cooperative hierarchical structures multiadaptive games
2011/1/5
We investigate a game-theoretic model of a social system where both the rules of the game and the interaction structure are shaped by the behavior of the agents. We call this type of model, with sever...
Similarity search for local protein structures at atomic resolution by exploiting a database management system
ligand binding sites structural alignment relational database geometric indexing Hungarian algorithm
2010/12/2
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time...
Prediction of interacting proteins from homology-modeled complex structures using sequence and structure scores
protein-protein interaction homology modeling binding specificity sequence similarity contact energy
2010/12/2
Protein-protein interactions support most biological processes, and it is important to find specifically interacting partner proteins among homologous proteins in order to elucidate cellular functions...
Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structures from amino acid sequences using critical random networks
protein structure prediction one-dimensional structure position-specific scoring matrix critical random network
2010/12/2
Predictions of one-dimensional protein structures such as secondary structures and contact numbers are useful for predicting three-dimensional structure and important for understanding the sequence-st...