With the progress of plant genome research, more than 50 plant metallothionein_like (MT_L) genes have been found, but only several MT_L proteins have been detected and no experimental structural information for MT_L p...With the progress of plant genome research, more than 50 plant metallothionein_like (MT_L) genes have been found, but only several MT_L proteins have been detected and no experimental structural information for MT_L proteins has been reported so far. Since detailed knowledge of the protein tertiary structure is required to understand its biological function, a method is needed to determine the structure of these proteins. In this study, the structural data of known mammal MT was used to determine the interatomic distance constraints of the CXC and CXXC motifs and the metal_sulfur chelating cluster. Then several possible MT conformations were predicted using a distance geometry algorithm. The statistical analysis was used to select those with much lower target function values and lower conformation energies as the predicted tertiary structural models of the cysteine_rich (CR) domains of these proteins. A suitable prediction method for modeling the CR domain of the plant MT_L protein was constructed. The accurately predicted result for the known structure of an MT protein from blue crab suggests that this method is practicable. The tertiary structures of CR domains of rape MT_L protein LSC54 was then modeled with this method.展开更多
The discovery of intrinsically disordered proteins （IDP） （i.e., biologically active proteins that do not possess stable secondary and/or tertiary structures） came as an unexpected surprise, as the existence of suc...The discovery of intrinsically disordered proteins （IDP） （i.e., biologically active proteins that do not possess stable secondary and/or tertiary structures） came as an unexpected surprise, as the existence of such proteins is in contradiction to the traditional ＂sequence →structure →function＂ paradigm. Accurate prediction of a protein＇s predisposition to be intrinsically disordered is a necessary prerequisite for the further understanding of principles and mechanisms of protein folding and function, and is a key for the elaboration of a new structural and functional hierarchy of proteins. Therefore, prediction of IDPs has attracted the attention of many researchers, and a number of prediction tools have been developed. Predictions of disorder, in turn, are playing major roles in directing laboratory experiments that are leading to the discovery of ever more disordered proteins, and thereby leading to a positive feedback loop in the investigation of these proteins. In this review of algorithms for intrinsic disorder prediction, the basic concepts of various prediction methods for IDPs are summarized, the strengths and shortcomings of many of the methods are analyzed, and the difficulties and directions of future development of IDP prediction techniques are discussed.展开更多
A novel algorithm to voxelize 3D mesh models with gray levels is presented in this paper.The key innovation of our method is to decide the gray level of a voxel according to the total area of all surfaces contained by...A novel algorithm to voxelize 3D mesh models with gray levels is presented in this paper.The key innovation of our method is to decide the gray level of a voxel according to the total area of all surfaces contained by it.During the preprocessing stage,a set of voxels in the extended bounding box of each triangle is established.Then we travel each triangle and compute the areas between it and its set of voxels one by one.Finally,each voxel is arranged a discrete gray level from 0 to 255.Experiments show that our algorithm gets a comparatively perfect result compared with the prevenient ones and approaches the original models in a more accurate way.展开更多
文摘With the progress of plant genome research, more than 50 plant metallothionein_like (MT_L) genes have been found, but only several MT_L proteins have been detected and no experimental structural information for MT_L proteins has been reported so far. Since detailed knowledge of the protein tertiary structure is required to understand its biological function, a method is needed to determine the structure of these proteins. In this study, the structural data of known mammal MT was used to determine the interatomic distance constraints of the CXC and CXXC motifs and the metal_sulfur chelating cluster. Then several possible MT conformations were predicted using a distance geometry algorithm. The statistical analysis was used to select those with much lower target function values and lower conformation energies as the predicted tertiary structural models of the cysteine_rich (CR) domains of these proteins. A suitable prediction method for modeling the CR domain of the plant MT_L protein was constructed. The accurately predicted result for the known structure of an MT protein from blue crab suggests that this method is practicable. The tertiary structures of CR domains of rape MT_L protein LSC54 was then modeled with this method.
文摘The discovery of intrinsically disordered proteins （IDP） （i.e., biologically active proteins that do not possess stable secondary and/or tertiary structures） came as an unexpected surprise, as the existence of such proteins is in contradiction to the traditional ＂sequence →structure →function＂ paradigm. Accurate prediction of a protein＇s predisposition to be intrinsically disordered is a necessary prerequisite for the further understanding of principles and mechanisms of protein folding and function, and is a key for the elaboration of a new structural and functional hierarchy of proteins. Therefore, prediction of IDPs has attracted the attention of many researchers, and a number of prediction tools have been developed. Predictions of disorder, in turn, are playing major roles in directing laboratory experiments that are leading to the discovery of ever more disordered proteins, and thereby leading to a positive feedback loop in the investigation of these proteins. In this review of algorithms for intrinsic disorder prediction, the basic concepts of various prediction methods for IDPs are summarized, the strengths and shortcomings of many of the methods are analyzed, and the difficulties and directions of future development of IDP prediction techniques are discussed.
基金the National Natural Science Foundation of China (60903111)
文摘A novel algorithm to voxelize 3D mesh models with gray levels is presented in this paper.The key innovation of our method is to decide the gray level of a voxel according to the total area of all surfaces contained by it.During the preprocessing stage,a set of voxels in the extended bounding box of each triangle is established.Then we travel each triangle and compute the areas between it and its set of voxels one by one.Finally,each voxel is arranged a discrete gray level from 0 to 255.Experiments show that our algorithm gets a comparatively perfect result compared with the prevenient ones and approaches the original models in a more accurate way.
