Physico-chemical approach to protein structure prediction by coarse-grained model
نویسندگان
چکیده
منابع مشابه
A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction.
De novo prediction of protein structures, the prediction of structures from amino acid sequences which are not similar to those of hitherto resolved structures, has been one of the major challenges in molecular biophysics. In this paper, we develop a new method of de novo prediction, which combines the fragment assembly method and the simulation of physical folding process: structures which hav...
متن کاملProtein secondary-structure description with a coarse-grained model.
A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(α) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(α) positions. Using ...
متن کاملProtein secondary structure analysis with a coarse-grained model
The paper presents a geometrical model for protein secondary structure analysis which uses only the positions of the Cα-atoms. We construct a space curve connecting these positions by piecewise polynomial interpolation and describe the folding of the protein backbone by a succession of screw motions linking the Frenet frames at consecutive Cα-positions. Using the ASTRAL subset of the SCOPe data...
متن کاملPrediction of protein structure by simulating coarse-grained folding pathways: a preliminary report.
A set of software tools designed to study protein structure and kinetics has been developed. The core of these tools is a program called Folding Machine (FM) which is able to generate low resolution folding pathways using modest computational resources. The FM is based on a coarse-grained kinetic ab initio Monte-Carlo sampler that can optionally use information extracted from secondary structur...
متن کاملFolding Trp-cage to NMR resolution native structure using a coarse-grained protein model.
We develop a coarse-grained protein model with a simplified amino acid interaction potential. Using this model, we perform discrete molecular dynamics folding simulations of a small 20-residue protein--Trp-cage--from a fully extended conformation. We demonstrate the ability of the Trp-cage model to consistently reach conformations within 2-angstroms backbone root-mean-square distance from the c...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Seibutsu Butsuri
سال: 2001
ISSN: 0582-4052,1347-4219
DOI: 10.2142/biophys.41.s15_2