e report a simple continuous potential function that can recognize proteinchains' native folds from tens of thousands of alternative ones. Empirical parame-ters for this potential function were obtained by a neura...e report a simple continuous potential function that can recognize proteinchains' native folds from tens of thousands of alternative ones. Empirical parame-ters for this potential function were obtained by a neural network learning oversamples generated from PDB structural data.Hydrophobic interactions were foundto be mainly responsible for stabilization of the protein' s native fold. The inter-chain interaction was found indispensable in stabilizing some protein chains' nativeconformation.展开更多
Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis o...Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis on known native structures of proteins. Many knowledge-based potentials for proteins have been proposed. Contrary to most existing review articles which mainly describe technical details and applications of various potential models, the main foci for the discussion here are ideas and concepts involving the construction of potentials, including the relation between free energy and energy, the additivity of potentials of mean force and some key issues in potential construction. Sequence analysis is briefly viewed from an energetic viewpoint.展开更多
In this work, we make an investigation on the preferences of orientations between amino acids using the orientation defined based on the local geometry of the amino acids concerned. It is found that there are common p...In this work, we make an investigation on the preferences of orientations between amino acids using the orientation defined based on the local geometry of the amino acids concerned. It is found that there are common preferences of orientations （70°, 30°, 140°） and （110°, 340°, 100°） for various pairs of amino acids. Different side chains may strengthen or weaken the common preferences, which is related to the effect of packing. Some amino acids having specific local flexibility may possess some preferences of orientations besides the common ones, such as （10°, 280°, 210°）. Another analysis on the pairs of the amino acids with different secondary-structure preferences shows that the directional interaction may affect the distribution of orientation more effectively than the packing or local flexibility. All these results provide us some insight of the organization of amino acids in protein, and their relation with some related interactions.展开更多
文摘e report a simple continuous potential function that can recognize proteinchains' native folds from tens of thousands of alternative ones. Empirical parame-ters for this potential function were obtained by a neural network learning oversamples generated from PDB structural data.Hydrophobic interactions were foundto be mainly responsible for stabilization of the protein' s native fold. The inter-chain interaction was found indispensable in stabilizing some protein chains' nativeconformation.
基金Project supported in part by the National Natural Science Foundation of China(Grant Nos.11175224 and 11121403)
文摘Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis on known native structures of proteins. Many knowledge-based potentials for proteins have been proposed. Contrary to most existing review articles which mainly describe technical details and applications of various potential models, the main foci for the discussion here are ideas and concepts involving the construction of potentials, including the relation between free energy and energy, the additivity of potentials of mean force and some key issues in potential construction. Sequence analysis is briefly viewed from an energetic viewpoint.
基金Project supported by the National Natural Science Foundation of China （Grant Nos 10204013, 90103031, 10074030, 10474041, 90403120 and 10021001）, and the Nonlinear Project （973） of the National Science Ministry, China.
文摘In this work, we make an investigation on the preferences of orientations between amino acids using the orientation defined based on the local geometry of the amino acids concerned. It is found that there are common preferences of orientations （70°, 30°, 140°） and （110°, 340°, 100°） for various pairs of amino acids. Different side chains may strengthen or weaken the common preferences, which is related to the effect of packing. Some amino acids having specific local flexibility may possess some preferences of orientations besides the common ones, such as （10°, 280°, 210°）. Another analysis on the pairs of the amino acids with different secondary-structure preferences shows that the directional interaction may affect the distribution of orientation more effectively than the packing or local flexibility. All these results provide us some insight of the organization of amino acids in protein, and their relation with some related interactions.
