Molecular Descriptors for Chemoinformatics: Volume I: Alphabetical Listing / Volume II: Appendices, References, Volume 41

1239 Pages·2008·8.93 MB·English

by  Raimund Mannhold

Roberto Todeschini and
Viviana Consonni
Molecular Descriptors for
Chemoinformatics
Methods and Principles in Medicinal Chemistry
Editedby R. Mannhold,H.Kubinyi, G.Folkers
EditorialBoard
H.Timmerman, J.Vacca, H.van de Waterbeemd, T.Wieland
Previous Volumes of this Series:
D.A.Smith, H.vande Waterbeemd, K.Wanner,G. Höfner(Eds.)
D.K.Walker
Mass Spectrometry in
Pharmacokinetics and Medicinal Chemistry
Metabolism in Drug Design,
Vol.36
2ndEd.
2007,ISBN978-3-527-31456-0
Vol.31
2006,ISBN978-3-527-31368-6 R.Mannhold (Ed.)
Molecular Drug Properties
T.Langer, R.D.Hofmann (Eds.)
Vol.37
Pharmacophores and
Pharmacophore Searches 2008,ISBN978-3-527-31755-4
Vol.32
R.J. Vaz,T.Klabunde (Eds.)
2006,ISBN978-3-527-31250-4 Antitargets
E.Francotte, W.Lindner (Eds.) Vol.38
Chirality in Drug Research 2008,ISBN978-3-527-31821-6
Vol.33
E.Ottow,H.Weinmann (Eds.)
2006,ISBN978-3-527-31076-0
Nuclear Receptors as
W.Jahnke, D. A.Erlanson(Eds.) Drug Targets
Fragment-based Approaches Vol.39
in Drug Discovery
2008,ISBN978-3-527-31872-8
Vol.34
H.van de Waterbeemd,
2006,ISBN978-3-527-31291-7
B.Testa (Eds.)
J.Hüser (Ed.) Drug Bioavailability,
High-Throughput Screening 2ndEd.
Vol.40
in Drug Discovery
Vol.35 2009,ISBN978-3-527-31872-8
2006,ISBN978-3-527-31283-2
Roberto Todeschini and Viviana Consonni
Molecular Descriptors for
Chemoinformatics
Volume II: Appendices, References
Second, Revised and Enlarged Edition
SeriesEditors AllbookspublishedbyWiley-VCHarecarefully
produced.Nevertheless,authors,editors,and
Prof.Dr.RaimundMannhold publisherdonotwarranttheinformationcontained
MolecularDrugResearchGroup inthesebooks,includingthisbook,tobefreeof
Heinrich-Heine-Universität errors.Readersareadvisedtokeepinmindthat
Universitätsstrasse1 statements,data,illustrations,proceduraldetailsor
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[email protected] #2009WILEY-VCHVerlagGmbH&Co.KGaA,
Weinheim
VolumeAuthors Allrightsreserved(includingthoseoftranslationinto
otherlanguages).Nopartofthisbookmaybe
Prof.Dr.RobertoTodeschini reproducedinanyform–byphotoprinting,
Dept.ofEnvironm.Sciences microfilm,oranyothermeans–nortransmittedor
UniversityMilano-Bicocca translatedintoamachinelanguagewithoutwritten
PiazzadellaScienza1 permissionfromthepublishers.Registerednames,
0126Milano trademarks,etc.usedinthisbook,evenwhennot
Italy specificallymarkedassuch,arenottobeconsidered
[email protected] unprotectedbylaw.
Dr.VivianaConsonni CoverDesign Grafik-DesignSchulz,Fußgönheim
Dept.Environm.Sciences Typesetting ThomsonDigital,Noida,India
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[email protected] Printedonacid-freepaper
ISBN978-3-527-31852-0
CoverDescription
Background:Frontofatabletfragment
ofamiddleAssyriancode.
Foreground:Drawingofphenylurea.
Thisbookisdedicatedwithloveto
Alessia,Davide,Edoardo,Marco,Milo,Marilena,andGiovanni
A good scientist should have the imagination of a child, the
determination of a boy, the rationality of a man, and the
experienceofanoldman.Thedifficultyistohaveallthesequalities
at the same time.
R.T.
Any alternative viewpoint with a different emphasis leads to an
inequivalent description. There is only one reality but there are
many points of view.
Itwouldbeverynarrow-mindedtouseonlyonecontext:wehaveto
learn to be able imagining points of view.
HansPrimasinChemistry,QuantumMechanicsand
Reductionism
(Springer-Verlag,1981)
VII
Contents
Volume I
Dedication V
TheAuthors IX
Acknowledgments X
Preface XI
APersonalForeword XIII
Introduction XV
HistoricalPerspective XXIII
QSAR/QSPRModeling XXVII
HowtoLearnFromThisBook XXXIII
User’sGuide XXXVII
NotationsandSymbols XXXIX
AlphabeticalListing
A 1
B 39
C 77
D 179
E 237
F 311
G 325
H 367
I 395
J 425
K 427
L 433
M 475
N 563
MolecularDescriptorsforChemoinformatics,VolumeII:Appendices,References
RobertoTodeschiniandVivianaConsonni
Copyright(cid:1)2009WILEY-VCHVerlagGmbH&Co.KGaA,Weinheim
ISBN:978-3-527-31852-0
VIII Contents
O 567
P 573
Q 613
R 637
S 659
T 799
U 833
V 835
W 875
X 951
Y 953
Z 955
GreekAlphabetEntries 961
NumericalEntries 963
Volume II
Bibliography 1
AppendixA 243
AppendixB 245
AppendixC 251
IX
The Authors
RobertoTodeschiniisfullprofessorofchemometricsatthe
DepartmentofEnvironmentalSciencesoftheUniversityof
Milano-Bicocca (Milano, Italy), where he constituted the
Milano Chemometrics and QSAR Research Group. His
main research activities concern chemometrics in all its
aspects, QSAR, molecular descriptors, multicriteria deci-
sion making, and software development. President of the
International Academy of Mathematical Chemistry, presi-
dentoftheItalianChemometricSociety,and“adhonorem”
professoroftheUniversityofAzuay(Cuenca,Ecuador),heisauthorofmorethan
170 publications in international journals and of the books ‘‘The Data Analysis
Handbook,’’ by I.E. Frank and R. Todeschini, 1994, and ‘‘Handbook of Molecular
Descriptors,’’byR.TodeschiniandV.Consonni,2000.
Viviana Consonni received her PhD in chemical sciences
from the University of Milano in 2000 and is now full
researcher of chemometrics and chemoinformatics at the
DepartmentofEnvironmentalSciencesoftheUniversityof
Milano-Bicocca (Milano, Italy). She is a member of the
Milano Chemometrics and QSAR Research Group and
has 10 years experience in multivariate analysis, QSAR,
molecular descriptors, multicriteria decision making, and
softwaredevelopment.Sheisauthorofmorethan40pub-
lications in peer-reviewed journals and of the book ‘‘Handbook of Molecular
Descriptors,’’ by R. Todeschini and V. Consonni, 2000. In 2006, she obtained the
InternationalAcademyofMathematicalChemistryAwardfordistinguishedyoung
researchers and, in June 2009, has been elected as youngest Member of the
Academy.
MolecularDescriptorsforChemoinformatics,VolumeII:Appendices,References
RobertoTodeschiniandVivianaConsonni
Copyright(cid:1)2009WILEY-VCHVerlagGmbH&Co.KGaA,Weinheim
ISBN:978-3-527-31852-0
X
Acknowledgments
The idea of producing the book Molecular Descriptors for Chemoinformatics was
welcomed by several colleagues whom we warmly thank for their suggestions,
revisions,bibliographicinformation,andmoralsupport;weareparticularlygrateful
to Alexander Balaban, Milan Randic´, and several members of the International
AcademyofMathematicalChemistry.
Particular thanks go also to Maurizio Bruschi, Ugo Cosentino, Mircea Diudea,
and Marco Vighi for their help in revising some topics of the book. The Authors
gratefullyacknowledgethecooperationwithandthesupportoftheeditorialstaffof
Wiley-VCH. In particular, we have to thank Nicola Oberbeckmann-Winter, Frank
Weinreich,CarolaSchmidt,SusannaPohl,ClaudiaNussbeck,WaltraudWüst.The
Authorsalso warmlythankRaymund Mannhold,editor oftheseries,forstimula-
tionsandtimelypressuretocompletethisbookontime.
Finally,sincewehavebeenfullyabsorbedinwritingthebookforalongtime,we
wouldliketoheartilyacknowledgeDavideBallabio,AndreaMauri,AlbertoManga-
naro, and Manuela Pavan of our team not only for their help but also for their
patienceandassistanceduringthisperiod.
XI
Preface
In 2000, Roberto Todeschini and Viviana Consonni wrote the highly valuable
Handbook of Molecular Descriptors, part of our series ‘‘Methods and Principles in
MedicinalChemistry.’’Thisvolumeachievedhighacceptanceamongresearchersin
the field of drug discovery and design. Now, eight years later, the significant
developments in the area of molecular descriptors necessitated a rather compre-
hensiverevision.
All new descriptors, QSAR approaches and chemometric strategies proposed
since 2000 have been included in this handbook. Several new topics such as
biodescriptors,characteristicpolynomial-baseddescriptors,propertyfilters,scoring
functions,andcell-basedmethodshavebeenadded.Othertopics,suchassubstruc-
turedescriptors,autocorrelationdescriptors,delocalizationdegreeindices,weighted
matrices,connectivityindices,andsoon,havebeencompletelyrewritten.
Attentionisalsopaidtorecentmethodsdedicatedtovirtualscreeningoflibraries
ofmolecules,suchascell-basedmethods,propertyfilters,andscoringfunctions.
Specialattentionhasbeenpaidtostrategiesforgeneratingfamiliesofmolecular
descriptors based on generalization of classical molecular descriptors; dedicated
entries are, for instance, Wiener-type indices, Randic´-like indices, Balaban-like
indices,connectivity-likeindices,andvariabledescriptors.
Severalentrieshavebeenjoinedtogetherinlargerentriesallowingeasierread-
ability and comparability among the different molecular descriptors; for example,
entriessuchasmatricesofmolecules,weightedmatrices,substructuredescriptors,
and vertex degrees, which were enlarged in order to include a lot of definitions.
Moreover, some didactical routes are introduced at the beginning of the book to
indicatethemainentriesconcerningatopic.
General entries concerning statistical indices, regression parameters, classifica-
tion parameters, similarity/diversity were completely rewritten trying to give an
exhaustiveviewofthefunctionsusedtocharacterizedata,modeling,andsimilarity/
diversityanalysis.Forexample,morethan50distanceandsimilarityfunctionshave
beenreported.
Numericalexamples(morethan150)andseveraltableslistingmoleculardescrip-
torsfortwobenchmarkdatasetsareaddedtohelpstudentsandnonexpertreadersto
comprehendthealgorithmsbetter.Indeed,thisneweditionhasbeenconceivednot
MolecularDescriptorsforChemoinformatics,VolumeII:Appendices,References
RobertoTodeschiniandVivianaConsonni
Copyright(cid:1)2009WILEY-VCHVerlagGmbH&Co.KGaA,Weinheim
ISBN:978-3-527-31852-0