The learning Bayesian network （BN） structure from data is an NP-hard problem and still one of the most exciting chal- lenges in the machine learning. In this work, a novel algorithm is presented which combines ideas...The learning Bayesian network （BN） structure from data is an NP-hard problem and still one of the most exciting chal- lenges in the machine learning. In this work, a novel algorithm is presented which combines ideas from local learning, constraint- based, and search-and-score techniques in a principled and ef- fective way. It first reconstructs the junction tree of a BN and then performs a K2-scoring greedy search to orientate the local edges in the cliques of junction tree. Theoretical and experimental results show the proposed algorithm is capable of handling networks with a large number of variables. Its comparison with the well-known K2 algorithm is also presented.展开更多
It has been well accepted that the folding energy landscape may resemble a funnel according to the theory of protein folding. This theory of ＂folding funnel＂ has been extensively studied and thought to play an impor...It has been well accepted that the folding energy landscape may resemble a funnel according to the theory of protein folding. This theory of ＂folding funnel＂ has been extensively studied and thought to play an important role in guiding the sampling process of the protein folding and refinement in protein structure prediction. Here, we have investigated the relationship between the ＂funnel likeness＂ of protein folding and the size/structure of the proteins based on a set of non-homologous proteins we have recently evaluated using a statistical mechanicsbased scoring function ITScorePro. It was found that larger proteins that consist of more helix/sheet structures tend to have a higher score-Root Mean Square Deviation（RMSD） correlation（or a more funnel like energy landscape）.Another measurement in protein folding, Z-score, has also shown some correlation with the size of the proteins.As expected, proteins with a better ＂olding funnel likeness＂（or score-RMSD correlation） tend to have a betterpredicted conformation with a lower RMSD from their native structures. These findings can be extremely valuable for the development and improvement of sampling and scoring algorithms for protein structure prediction.展开更多
A noval molecular structural expression method,three-dimensional vector of atomic interac-tion field(3D-VAIF),has been newly developed based on electrostatic and steric interaction between different types of atoms.Fea...A noval molecular structural expression method,three-dimensional vector of atomic interac-tion field(3D-VAIF),has been newly developed based on electrostatic and steric interaction between different types of atoms.Feature descriptors of single amino acid,i.e.principal component scores of struc-tural information for amino acids(SSIA),are obtained through calculation of structural information of 20 coded amino acids using principal component analy-sis(PCA)method,and the strict tests are performed on the property of SSIA by three quantitative struc-ture-activity relationships(QSARs)/quantitative se-quence-activity models(QSAMs)models of 58 ngio-tensin-converting enzymes(ACE),48 bitter tasting thresholds(BTT)and 31 bradykinin potentiating pentapeptides(BPP).Cumulative multiple correlation coefficients(Rc2um)are 0.789,0.856 and 0.838;and corresponding cross-validated correlation coefficients(QL2OO)are 0.773,0.837 and 0.815,respectively.Good results indicate that SSIA are better than tradi-tional descriptors of amino acid in quantitative se-quence-activity relationships of peptide analogues.展开更多
基金supported by the National Natural Science Fundation of China (6097408261075055)the Fundamental Research Funds for the Central Universities (K50510700004)
文摘The learning Bayesian network （BN） structure from data is an NP-hard problem and still one of the most exciting chal- lenges in the machine learning. In this work, a novel algorithm is presented which combines ideas from local learning, constraint- based, and search-and-score techniques in a principled and ef- fective way. It first reconstructs the junction tree of a BN and then performs a K2-scoring greedy search to orientate the local edges in the cliques of junction tree. Theoretical and experimental results show the proposed algorithm is capable of handling networks with a large number of variables. Its comparison with the well-known K2 algorithm is also presented.
文摘It has been well accepted that the folding energy landscape may resemble a funnel according to the theory of protein folding. This theory of ＂folding funnel＂ has been extensively studied and thought to play an important role in guiding the sampling process of the protein folding and refinement in protein structure prediction. Here, we have investigated the relationship between the ＂funnel likeness＂ of protein folding and the size/structure of the proteins based on a set of non-homologous proteins we have recently evaluated using a statistical mechanicsbased scoring function ITScorePro. It was found that larger proteins that consist of more helix/sheet structures tend to have a higher score-Root Mean Square Deviation（RMSD） correlation（or a more funnel like energy landscape）.Another measurement in protein folding, Z-score, has also shown some correlation with the size of the proteins.As expected, proteins with a better ＂olding funnel likeness＂（or score-RMSD correlation） tend to have a betterpredicted conformation with a lower RMSD from their native structures. These findings can be extremely valuable for the development and improvement of sampling and scoring algorithms for protein structure prediction.
基金This work was supported by Fok-Yingtung Educational Foundation(Grant No.98-7-6)Na-tional Chunhui Project Foundation(Grant No.99-4-4+37)+1 种基金Chongqing Applied Fundamental Science Fund(Grant No.01-3-6)Chongqing University Innovation Foundation of Science and Technology(Grant No.03-5-6+04-9-1).
文摘A noval molecular structural expression method,three-dimensional vector of atomic interac-tion field(3D-VAIF),has been newly developed based on electrostatic and steric interaction between different types of atoms.Feature descriptors of single amino acid,i.e.principal component scores of struc-tural information for amino acids(SSIA),are obtained through calculation of structural information of 20 coded amino acids using principal component analy-sis(PCA)method,and the strict tests are performed on the property of SSIA by three quantitative struc-ture-activity relationships(QSARs)/quantitative se-quence-activity models(QSAMs)models of 58 ngio-tensin-converting enzymes(ACE),48 bitter tasting thresholds(BTT)and 31 bradykinin potentiating pentapeptides(BPP).Cumulative multiple correlation coefficients(Rc2um)are 0.789,0.856 and 0.838;and corresponding cross-validated correlation coefficients(QL2OO)are 0.773,0.837 and 0.815,respectively.Good results indicate that SSIA are better than tradi-tional descriptors of amino acid in quantitative se-quence-activity relationships of peptide analogues.
