Novel amino acids indices based on quantum topological molecular similarity and their application to QSAR study of peptides

Amino Acids

Volumn 40, Issue 4, 2011, Pages 1169-1183

  Hemmateenejad, Bahram ^a,b   Yousefinejad, Saeed ^a,b   Mehdipour, Ahmad Reza ^b  

^a SHIRAZ UNIVERSITY   (Iran)

^b SHIRAZ UNIVERSITY OF MEDICAL SCIENCES   (Iran)

Author keywords

Amino acid indices; Peptide; QSAR; QTMS

Indexed keywords

AMINO ACID; BACTERICIDAL PEPTIDE; DIPEPTIDYL CARBOXYPEPTIDASE INHIBITOR; HLA A ANTIGEN; PEPTIDE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL STRUCTURE; CONTROLLED STUDY; ENZYME ACTIVE SITE; GENETIC ALGORITHM; PARTIAL LEAST SQUARES REGRESSION; PREDICTIVE VALUE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN LOCALIZATION; QAUNTUM TOPOLOGICAL MOLECULAR SIMILARITY; QUANTITATIVE STRUCTURE ACTIVITY RELATION; QUANTUM CHEMISTRY; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; AMINO ACIDS; ANGIOTENSIN-CONVERTING ENZYME INHIBITORS; ANTI-BACTERIAL AGENTS; CATALYTIC DOMAIN; HLA-A ANTIGENS; HUMANS; LEAST-SQUARES ANALYSIS; MODELS, CHEMICAL; PEPTIDES; PRINCIPAL COMPONENT ANALYSIS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; QUANTUM THEORY;

EID: 79954435535     PISSN: 09394451     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00726-010-0741-x     Document Type: Article

References (39)

1. BK Alsberg N Marchand-Geneste RD King 2000 A new 3D molecular structure representation using quantum topology with application to structure-property relationships Chemom Intell Lab Syst 54 75 91 10.1016/S0169-7439(00)00101-5 1:CAS:528:DC%2BD3MXit12gt7c%3D (Pubitemid 32062994)
2. BK Alsberg N Marchand-Geneste RD King 2001 Modeling quantitative structure-property relationships in calculated reaction pathways using a new 3D quantum topological representation Anal Chim Acta 446 3 13 10.1016/S0003- 2670(01)00984-9 1:CAS:528:DC%2BD3MXoslert7c%3D (Pubitemid 33042651)
3. Bader RFW (1990) Atoms in molecules: a quantum theory. Oxford University Press, Oxford
4. RFW Bader HJT Preston 1969 The kinetic energy of molecular charge distributions and molecular stability Int J Quantum Chem 3 327 347 10.1002/qua.560030308 1:CAS:528:DyaF1MXkt1CkurY%3D
5. RFW Bader TT Nguyen-Dang Y Tal 1981 A topological theory of molecular structure Rep Prog Phys 44 893 948 10.1088/0034-4885/44/8/002
6. K Baumann 2003 Cross-validation as the objective function for variable-selection techniques Trends Anal Chem 22 395 406 10.1016/S0165-9936(03) 00607-1 1:CAS:528:DC%2BD3sXks1WrsL8%3D (Pubitemid 36694985)
7. K Baumann 2005 Chance correlation in variable subset regression: influence of the objective function, the selection mechanism, and ensemble averaging QSAR Comb Sci 24 1033 1046 10.1002/qsar.200530134 1:CAS:528: DC%2BD2MXhtlWmsbzL (Pubitemid 41736469)
8. I Bytheway PLA Popelier RJ Gillespie 1996 Topological studies of the charge density of some group 2 metallocenes M(η5-C5H5)2 (M = Mg or Ca) Can J Chem 74 1059 1071 10.1139/v96-119 1:CAS:528:DyaK28Xks1yrt70%3D (Pubitemid 126423920)
9. UA Chaudry PLA Popelier 2003 Ester hydrolysis rate constant prediction from quantum topological molecular similarity (QTMS) descriptors J Phys Chem A 107 4578 4582 10.1021/jp034272a 1:CAS:528:DC%2BD3sXjsFKrsr4%3D
10. IA Doytchinova V Walshe P Borrow DR Flower 2005 Towards the chemometric dissection of peptide-HLA-A*0201 binding affinity: comparison of local and global QSAR models J Comput-Aided Mol Des 19 203 212 16059672 10.1007/s10822-005-3993-x 1:CAS:528:DC%2BD2MXls1Smsrs%3D (Pubitemid 40974007)
11. QS Du RB Huang KC Chou 2008 Recent advances in QSAR and their applications in predicting the activities of chemical molecules, peptides and proteins for drug design Curr Protein Pept Sci 9 248 260 18537680 10.2174/138920308784534005 1:CAS:528:DC%2BD1cXlsFens74%3D (Pubitemid 351997841)
12. Erikson L, Johansson E, Kettaneh-Wold N, Wold S (2001) Multi- and mega-variate data analysis. Principle and applications. Umetrics Academy, Umea
13. C Hansch D Hoekman A Leo D Weininger CD Selassie 2002 Chem-bioinformatics: comparative QSAR at the interface between chemistry and biology Chem Rev 102 783 812 11890757 10.1021/cr0102009 1:CAS:528: DC%2BD38XhtVWksb8%3D (Pubitemid 35377614)
14. AP Harding DC Wedge PLA Popelier 2009 pKa prediction from "Quantum Chemical Topology" descriptors J. Chem Inf Model 49 1914 1924 19630371 10.1021/ci900172h 1:CAS:528:DC%2BD1MXovFKmu7c%3D
15. B Hemmateenejad 2005 Correlation ranking procedure for factor selection in PC-ANN modeling and application to ADMETox evaluation Chemom Intell Lab Syst 75 231 245 10.1016/j.chemolab.2004.09.005 1:CAS:528:DC%2BD2MXmtFOrsA%3D%3D (Pubitemid 40164345)
16. B Hemmateenejad A Mohajeri 2007 Application of quantum topological molecular similarity descriptors in QSPR study of the O-methylation of substituted phenols J Comput Chem 29 266 274 10.1002/jcc.20787
17. B Hemmateenejad M Akhond R Miri M Shamsipur 2003 Genetic algorithm applied to the selection of factors in principal component-artificial neural networks: application to QSAR study of calcium channel antagonist activity of 1,4-dihydropyridines (nifedipine analogous) J Chem Inf Comput Sci 43 1328 1334 12870926 1:CAS:528:DC%2BD3sXkvVaiur4%3D
18. B Hemmateenejad AR Mehdipour PLA Popelier 2008 Quantum topological QSAR models based on the MOLMAP approach Chem Biol Drug Des 72 551 563 19090922 10.1111/j.1747-0285.2008.00731.x 1:CAS:528:DC%2BD1cXhsFemtLvL
19. H Jenssen TJ Gutteberg Ø Rekdal T Lejon 2006 Prediction of activity, synthesis and biological testing of anti-HSV active peptides Chem Biol Drug Des 68 58 66 16923027 10.1111/j.1747-0285.2006.00412.x 1:CAS:528:DC%2BD28XhtVOjur%2FL (Pubitemid 44272820)
20. ZH Lin HX Long Z Bo YQ Wang YZ Wu 2008 New descriptors of amino acids and their application to peptide QSAR study Peptides 29 1798 1805 18606203 10.1016/j.peptides.2008.06.004 1:CAS:528:DC%2BD1cXhtFCkurvM
21. A Mauri D Ballabio V Consonni A Managanaro R Todeschini 2008 Peptides multivariate characterization using a molecular based approach MATCH Commun Math Comput Chem 60 671 690 1:CAS:528:DC%2BD1MXislWjsLw%3D
22. AR Mehdipour B Hemmateenejad R Miri 2007 QSAR studies on the anesthetic action of some polyhalogenated ethers Chem Biol Drug Des 69 362 368 17539829 10.1111/j.1747-0285.2007.00506.x 1:CAS:528:DC%2BD2sXmsFeqtLw%3D (Pubitemid 46817450)
23. H Mei Y Zhou LL Sun ZL Li 2004 A new descriptor of amino acid and its application in peptide QSAR Acta Phys Chim Sin 20 821 825 1:CAS:528: DC%2BD2cXmvFCgsb0%3D (Pubitemid 39163767)
24. A Mohajeri B Hemmateenejad A Mehdipour R Miri 2008 Modeling calcium channel antagonistic activity of dihydropyridine derivatives using QTMS indices analyzed by GA-PLS and PC-GA-PLS J Mol Graph Model 26 1057 1065 17959402 10.1016/j.jmgm.2007.09.002 1:CAS:528:DC%2BD1cXjtlyjtLs%3D (Pubitemid 351374846)
25. SE O'Brien PLA Popelier 2001 Quantum molecular similarity 3. QTMS descriptors J Chem Inf Comput Sci 41 764 775 11410057
26. SE O'Brien PLA Popelier 2002 Quantum topological molecular similarity. Part 4. A QSAR study of cell growth inhibitory properties of substituted (E)-1-phenylbut-1-en-3-ones J Chem Soc Perkin Trans 2 478 483 (Pubitemid 35188217)
27. JA Padron-Garcia M Alonso-Tarajano E Alonso-Becerra TJ Winterburn R Yasser J Kay C Berry 2009 Quantitative structure activity relationship of IA3-like peptides as aspartic proteinase inhibitors Proteins 75 859 869 19003993 10.1002/prot.22295 1:CAS:528:DC%2BD1MXltleks7g%3D
28. PLA Popelier PJ Smith 2006 QSAR models based on quantum topological molecular similarity Eur J Med Chem 41 862 873 16697489 10.1016/j.ejmech.2006. 03.004 1:CAS:528:DC%2BD28XmvFelt74%3D (Pubitemid 44040954)
29. PLA Popelier UA Chaudry PJ Smith 2002 Quantum topological molecular similarity. Part 5: further development with an application to the toxicity of polychlorinated dibenzo-p-dioxins (PCDDs) J Chem Soc Perkin II 1231 1237 (Pubitemid 35188105)
30. PLA Popelier UA Chaudry PJ Smith 2004 Quantitative structure-activity relationships of mutagenic activity from quantum topological descriptors: triazenes and halogenated hydroxyfuranones (mutagen-X) derivatives J Comput-Aided Mol Des 18 709 718 15865063 10.1007/s10822-004-6815-7 1:CAS:528:DC%2BD2MXitFertrw%3D (Pubitemid 40425041)
31. M Rafat M Shaik PLA Popelier 2006 Transferability of quantum topological atoms in terms of electrostatic interaction energy J Phys Chem A 110 13578 13583 17165885 10.1021/jp0652190 1:CAS:528:DC%2BD28Xht1antbnN (Pubitemid 46196895)
32. R Ramos de Armas H González Díaz R Molina E Uriarte 2005 Stochastic-based descriptors studying biopolymers biological properties: extended MARCH-INSIDE methodology describing antibacterial activity of lactoferricin derivatives Biopolymers 77 247 256 10.1002/bip.20202 (Pubitemid 40546897)
33. K Roy PLA Popelier 2008 Exploring predictive QSAR models using quantum topological molecular similarity (QTMS) descriptors for toxicity of nitroaromatics to Saccharomyces cerevisiae QSAR Comb Sci 27 1006 1012 10.1002/qsar.200810028 1:CAS:528:DC%2BD1cXhtV2rur7M
34. K Roy PLA Popelier 2008 Exploring predictive QSAR models for hepatocyte toxicity of phenols using QTMS descriptors Bioorg Med Chem Lett 18 2604 2609 18378448 10.1016/j.bmcl.2008.03.035 1:CAS:528:DC%2BD1cXks1akt78%3D (Pubitemid 351506518)
35. CD Selassie SB Mekapati RP Verma 2002 QSAR: then and now Curr Top Med Chem 2 1357 1379 12470285 10.2174/1568026023392823 1:CAS:528: DC%2BD38Xos1Gjsr4%3D
36. F Tian L Yang F Lv Q Yang P Zhou 2009 In silico quantitative prediction of peptides binding affinity to human MHC molecule: an intuitive quantitative structure-activity relationship approach Amino Acids 36 535 554 18575802 10.1007/s00726-008-0116-8 1:CAS:528:DC%2BD1MXisVOku78%3D
37. J Tong S Liu P Zhou B Wu Z Li 2008 A novel descriptor of amino acids and its application in peptide QSAR J Theor Biol 253 90 97 18397794 10.1016/j.jtbi.2008.02.030 1:CAS:528:DC%2BD1cXnt1ertbg%3D
38. S Wold M Sjostrom L Eriksson 2001 PLS-regression: a basic tool of chemometrics Chemom Intell Lab Syst 58 109 130 10.1016/S0169-7439(01)00155-1 1:CAS:528:DC%2BD3MXotF2mtLw%3D (Pubitemid 33033283)
39. P Zhou X Chen Y Wu Z Shang 2010 Gaussian process: an alternative approach for QSAM modeling of peptides Amino Acids 38 199 212 19123053 10.1007/s00726-008-0228-1 1:CAS:528:DC%2BC3cXhtVehtb0%3D