Enlightened by the law of interactions among objects in the physical world, we propose a heuristic algorithm for solving the three-dimensional (3D) off-lattice protein folding problem. Based on a physical model, the p...Enlightened by the law of interactions among objects in the physical world, we propose a heuristic algorithm for solving the three-dimensional (3D) off-lattice protein folding problem. Based on a physical model, the problem is converted from a nonlinear constraint-satisfied problem to an unconstrained optimization problem which can be solved by the well-known gra- dient method. To improve the efficiency of our algorithm, a strategy was introduced to generate initial configuration. Computa- tional results showed that this algorithm could find states with lower energy than previously proposed ground states obtained by nPERM algorithm for all chains with length ranging from 13 to 55.展开更多
The "relative entropy" has been used as a minimization function to predict the tertiary structure of a protein backbone, and good results have been obtained. However, in our previous work, the ensemble avera...The "relative entropy" has been used as a minimization function to predict the tertiary structure of a protein backbone, and good results have been obtained. However, in our previous work, the ensemble average of the contact potential was estimated by an approximate calculation. In order to improve the theoretical integrity of the relative-entropy-based method, a new theoretical calculation method of the ensemble average of the contact potential was presented in this work, which is based on the thermodynamic perturbation theory. Tests of the improved algorithm were performed on twelve small proteins. The root mean square deviations of the predicted versus the native structures from Protein Data Bank range from 0.40 to 0.60 nm. Compared with the previous approximate values, the average prediction accuracy is improved by 0.04 nm.展开更多
Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one...Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one of the main tasks in modern biophysics. Coarse-grained methods play an increasingly important role in the simulation of protein folding, especially for large proteins. In recent years, we proposed a novel coarse-grained method derived from the topological soliton model, in terms of the backbone Cα chain. In this review, we will first systematically address the theoretical method of topological soliton. Then some successful applications will be displayed, including the thermodynamics simulation of protein folding, the property analysis of dynamic conformations, and the multi-scale simulation scheme. Finally, we will give a perspective on the development and application of topological soliton.展开更多
基金Project supported by the National Basic Research Program (973) of China (No. 2004CB318000) and the National Natural Science Foun-dation of China (No. 10471051)
文摘Enlightened by the law of interactions among objects in the physical world, we propose a heuristic algorithm for solving the three-dimensional (3D) off-lattice protein folding problem. Based on a physical model, the problem is converted from a nonlinear constraint-satisfied problem to an unconstrained optimization problem which can be solved by the well-known gra- dient method. To improve the efficiency of our algorithm, a strategy was introduced to generate initial configuration. Computa- tional results showed that this algorithm could find states with lower energy than previously proposed ground states obtained by nPERM algorithm for all chains with length ranging from 13 to 55.
基金Supported by the National Natural Science Foundation of China (Grant No.30670497)the Beijing Natural Science Foundation (Grant No.5072002)the Specialized Research Foundation for the Doctoral Program of Higher Education (Grant No.200800050003)
文摘The "relative entropy" has been used as a minimization function to predict the tertiary structure of a protein backbone, and good results have been obtained. However, in our previous work, the ensemble average of the contact potential was estimated by an approximate calculation. In order to improve the theoretical integrity of the relative-entropy-based method, a new theoretical calculation method of the ensemble average of the contact potential was presented in this work, which is based on the thermodynamic perturbation theory. Tests of the improved algorithm were performed on twelve small proteins. The root mean square deviations of the predicted versus the native structures from Protein Data Bank range from 0.40 to 0.60 nm. Compared with the previous approximate values, the average prediction accuracy is improved by 0.04 nm.
文摘Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one of the main tasks in modern biophysics. Coarse-grained methods play an increasingly important role in the simulation of protein folding, especially for large proteins. In recent years, we proposed a novel coarse-grained method derived from the topological soliton model, in terms of the backbone Cα chain. In this review, we will first systematically address the theoretical method of topological soliton. Then some successful applications will be displayed, including the thermodynamics simulation of protein folding, the property analysis of dynamic conformations, and the multi-scale simulation scheme. Finally, we will give a perspective on the development and application of topological soliton.
