Systematic studies are made on application of chemometrics to chemical modeling and/or molecular modeling as well as the regularity of retention index for gas chromatography (GC). A set of novel molecular graph theore...Systematic studies are made on application of chemometrics to chemical modeling and/or molecular modeling as well as the regularity of retention index for gas chromatography (GC). A set of novel molecular graph theoretical parameters, called the molecular distance-edge (MDE) vector (λ), is proposed ad found to be excellently correlated to retention index of GC for alkanes. The MDE parameters were tested by the multiple linear regression (MLR) estimation and production of the retention index of GC, and the results obtained are satisfactory.展开更多
A quantative relationship exists between the structrue and physical properties of organic compounds.The molecular structrue of the examined compounds is selectively described by a molecular distance-edge（MDE）vector....A quantative relationship exists between the structrue and physical properties of organic compounds.The molecular structrue of the examined compounds is selectively described by a molecular distance-edge（MDE）vector.The physical properties of alkanes such as boiling points,density at 25℃,refractive index at 25℃, heat capacity at 300K,Gibbs energy,enthalpy at 300K are estimated with satisfactory results by a novel modified back- propagation neural network method based on the above MDEvectot.展开更多
Only from the primary structures of peptides, a new set of descriptors called the molecular electro-negativity edge-distance vector (VMED) was proposed and applied to describing and characterizing the molecular struct...Only from the primary structures of peptides, a new set of descriptors called the molecular electro-negativity edge-distance vector (VMED) was proposed and applied to describing and characterizing the molecular structures of oligopeptides and polypeptides, based on the electronegativity of each atom or electronic charge index (ECI) of atomic clusters and the bonding distance between atom-pairs. Here, the molecular structures of antigenic polypeptides were well expressed in order to propose the auto-mated technique for the computerized identification of helper T lymphocyte (Th) epitopes. Furthermore, a modified MED vector was proposed from the primary structures of polypeptides, based on the ECI and the relative bonding distance of the fundamental skeleton groups. The side-chains of each amino acid were here treated as a pseudo-atom. The developed VMED was easy to calculate and able to work. Some quantitative model was established for 28 immunogenic or antigenic polypeptides (AGPP) with 14 (1― 14) Ad and 14 other restricted activities assigned as "1"(+) and "0"(-), respectively. The latter comprised 6 Ab(15-20), 3 Ak(21-23), 2 Ek(24-26), 2 H-2k(27 and 28) restricted sequences. Good results were obtained with 90% correct classification (only 2 wrong ones for 20 training samples) and 100% correct prediction(none wrong for 8 testing samples); while con-trastively 100% correct classification (none wrong for 20 training samples) and 88% correct classification (1 wrong for 8 testing samples). Both stochastic samplings and cross valida-tions were performed to demonstrate good performance. The described method may also be suitable for estimation and prediction of classes I and II for major histocompatibility an-tigen (MHC) epitope of human. It will be useful in immune identification and recognition of pro-teins and genes and in the design and devel-opment of subunit vaccines. Several quantitative structure activity relationship (QSAR) models were developed for various oligopeptides and polypeptides including 58 dipeptides and 31 pentapeptides with angiotensin converting enzyme (ACE) inhibition by multiple linear regression (MLR) method. In order to explain the ability to characterize molecular structure of polypeptides, a molecular modeling investigation on QSAR was performed for functional prediction of polypeptide sequences with anti-genic activity and heptapeptide sequences with tachykinin activity through quantitative se-quence-activity models (QSAMs) by the molecular electronegativity edge-distance vector (VMED). The results showed that VMED exhibited both excellent structural selectivity and good activity prediction. Moreover, the results showed that VMED behaved quite well for both QSAR and QSAM of poly-and oli-gopeptides, which exhibited both good estimation ability and prediction power, equal to or better than those reported in the previous references. Finally, a preliminary conclusion was drwan: both classical and modified MED vectors were very useful structural descriptors. Some suggestions were proposed for further studies on QSAR/QSAM of proteins in various fields.展开更多
Based on the identical group as a pseudo atom instead of a typical atom, a novel modified molecular dis-tance-edge (MDE) vector μ was developed in our laboratory to characterize chemical structure of polychlorinated ...Based on the identical group as a pseudo atom instead of a typical atom, a novel modified molecular dis-tance-edge (MDE) vector μ was developed in our laboratory to characterize chemical structure of polychlorinated diben-zofurans (PCDFs) congeners and/or isomers. Quantitative structure-retention relationships (QSRRs) between the new VMDE parameters and gas chromatographic (GC) retention behavior of PCDFs were then generated by multiple linear regression (MLR) method for non-polar, moderately polar, and polar stationary phases. Four excellent models with high correlation coefficients, R=0.984-0.995, were proposed for non-polar columns (DB-5, SE-54, OV-101). For the moder-ately polar columns (OV-1701), the correlation coefficient of the developed good model is only 0.958. For the polar col-umns (SP-2300), the QSRR model is poor with R=0.884. Then cross validation with leave-one out of procedure (CV) is performed in high correlation with the non-polar (Rcv=992-0.974) and weakly polar (Rcv=921) columns and in little cor-relation (Rcv=0.834) with the polar columns. These results show that the new μ vector is suitable for describing the re-tention behaviors of PCDFs on non-polar and moderately polar stationary phases and not for the various gas chroma-tographic retention behaviors of PCDFs on the different po-larity-varying stationary phases.展开更多
基金Project supported by the National Natural Science Foundation of China (No. 29775001 )the Ministry of Mechanical Industries Fund and Hoy Yinh-Tong Educational Foundation
文摘Systematic studies are made on application of chemometrics to chemical modeling and/or molecular modeling as well as the regularity of retention index for gas chromatography (GC). A set of novel molecular graph theoretical parameters, called the molecular distance-edge (MDE) vector (λ), is proposed ad found to be excellently correlated to retention index of GC for alkanes. The MDE parameters were tested by the multiple linear regression (MLR) estimation and production of the retention index of GC, and the results obtained are satisfactory.
文摘A quantative relationship exists between the structrue and physical properties of organic compounds.The molecular structrue of the examined compounds is selectively described by a molecular distance-edge（MDE）vector.The physical properties of alkanes such as boiling points,density at 25℃,refractive index at 25℃, heat capacity at 300K,Gibbs energy,enthalpy at 300K are estimated with satisfactory results by a novel modified back- propagation neural network method based on the above MDEvectot.
基金Supported by National High-Tech R&D Programme of China (863) (Grant No. 2006AA02Z312)National 111 Programme Introducing Talents of Discipline to Universities (Grant No. 0507111106)+6 种基金National Chunhui Project (Grant No. 990404+00307)State New Drug Project (Grant No. 1996ND1035A01)Fok YingTung Educational Foundation (Grant No. 980706)State Key Laboratory of Chemo/Biosensing and Chemometrics Foundation (KCBCF0501201)Chongqing University Innovation Fund (CUIF030506)Chongqing Municipality Applied Science Fund (Grant No. CASF01-3-6)Momentous Juche Innovation Fundfor Tackle Key Problem Items (MJIF 03-5-6+04-10-10)
文摘Only from the primary structures of peptides, a new set of descriptors called the molecular electro-negativity edge-distance vector (VMED) was proposed and applied to describing and characterizing the molecular structures of oligopeptides and polypeptides, based on the electronegativity of each atom or electronic charge index (ECI) of atomic clusters and the bonding distance between atom-pairs. Here, the molecular structures of antigenic polypeptides were well expressed in order to propose the auto-mated technique for the computerized identification of helper T lymphocyte (Th) epitopes. Furthermore, a modified MED vector was proposed from the primary structures of polypeptides, based on the ECI and the relative bonding distance of the fundamental skeleton groups. The side-chains of each amino acid were here treated as a pseudo-atom. The developed VMED was easy to calculate and able to work. Some quantitative model was established for 28 immunogenic or antigenic polypeptides (AGPP) with 14 (1― 14) Ad and 14 other restricted activities assigned as "1"(+) and "0"(-), respectively. The latter comprised 6 Ab(15-20), 3 Ak(21-23), 2 Ek(24-26), 2 H-2k(27 and 28) restricted sequences. Good results were obtained with 90% correct classification (only 2 wrong ones for 20 training samples) and 100% correct prediction(none wrong for 8 testing samples); while con-trastively 100% correct classification (none wrong for 20 training samples) and 88% correct classification (1 wrong for 8 testing samples). Both stochastic samplings and cross valida-tions were performed to demonstrate good performance. The described method may also be suitable for estimation and prediction of classes I and II for major histocompatibility an-tigen (MHC) epitope of human. It will be useful in immune identification and recognition of pro-teins and genes and in the design and devel-opment of subunit vaccines. Several quantitative structure activity relationship (QSAR) models were developed for various oligopeptides and polypeptides including 58 dipeptides and 31 pentapeptides with angiotensin converting enzyme (ACE) inhibition by multiple linear regression (MLR) method. In order to explain the ability to characterize molecular structure of polypeptides, a molecular modeling investigation on QSAR was performed for functional prediction of polypeptide sequences with anti-genic activity and heptapeptide sequences with tachykinin activity through quantitative se-quence-activity models (QSAMs) by the molecular electronegativity edge-distance vector (VMED). The results showed that VMED exhibited both excellent structural selectivity and good activity prediction. Moreover, the results showed that VMED behaved quite well for both QSAR and QSAM of poly-and oli-gopeptides, which exhibited both good estimation ability and prediction power, equal to or better than those reported in the previous references. Finally, a preliminary conclusion was drwan: both classical and modified MED vectors were very useful structural descriptors. Some suggestions were proposed for further studies on QSAR/QSAM of proteins in various fields.
基金This work was supported by the Chunhui Project Fund of the Ministry of Education(Grant No.SCPF99-4-4+37)Fok Ying-Tung Educational Foundation(Grant No.FYTF98-7-6)+1 种基金Chongqing Applied Science Fund(Grant No,CASF01-3-6)Chongqing University ZYXT Innovation Fund(Grant No.CUIF03-5-6+04-10-10).
文摘Based on the identical group as a pseudo atom instead of a typical atom, a novel modified molecular dis-tance-edge (MDE) vector μ was developed in our laboratory to characterize chemical structure of polychlorinated diben-zofurans (PCDFs) congeners and/or isomers. Quantitative structure-retention relationships (QSRRs) between the new VMDE parameters and gas chromatographic (GC) retention behavior of PCDFs were then generated by multiple linear regression (MLR) method for non-polar, moderately polar, and polar stationary phases. Four excellent models with high correlation coefficients, R=0.984-0.995, were proposed for non-polar columns (DB-5, SE-54, OV-101). For the moder-ately polar columns (OV-1701), the correlation coefficient of the developed good model is only 0.958. For the polar col-umns (SP-2300), the QSRR model is poor with R=0.884. Then cross validation with leave-one out of procedure (CV) is performed in high correlation with the non-polar (Rcv=992-0.974) and weakly polar (Rcv=921) columns and in little cor-relation (Rcv=0.834) with the polar columns. These results show that the new μ vector is suitable for describing the re-tention behaviors of PCDFs on non-polar and moderately polar stationary phases and not for the various gas chroma-tographic retention behaviors of PCDFs on the different po-larity-varying stationary phases.
