docs/refs.bib
% ABCIndex
@article{furtula_atom-bond_2016,
title = {Atom-bond connectivity index versus {Graovac}-{Ghorbani} analog},
volume = {75},
url = {http://match.pmf.kg.ac.rs/electronic_versions/Match75/n1/match75n1_233-242.pdf},
urldate = {2016-01-29},
journal = {MATCH Commun. Math. Comput. Chem},
author = {Furtula, Boris},
year = {2016},
pages = {233--242},
file = {match75n1_233-242.pdf:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/NWJBN5PN/match75n1_233-242.pdf:application/pdf}
}
% CPSA
@article{10.1021/ac00220a013,
title = {Development and use of charged partial surface area structural descriptors in computer-assisted quantitative structure-property relationship studies},
volume = {62},
issn = {0003-2700},
url = {http://dx.doi.org/10.1021/ac00220a013},
doi = {10.1021/ac00220a013},
number = {21},
urldate = {2016-02-02},
journal = {Analytical Chemistry},
author = {Stanton, David T. and Jurs, Peter C.},
month = nov,
year = {1990},
pages = {2323--2329},
file = {ACS Full Text PDF:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/H9AZDQM8/Stanton と Jurs - 1990 - Development and use of charged partial surface are.pdf:application/pdf;ACS Full Text Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/BRZAENGV/ac00220a013.html:text/html}
}
% EState
@article{10.1021/ci00028a014,
title = {Electrotopological {State} {Indices} for {Atom} {Types}: {A} {Novel} {Combination} of {Electronic}, {Topological}, and {Valence} {State} {Information}},
volume = {35},
issn = {0095-2338},
shorttitle = {Electrotopological {State} {Indices} for {Atom} {Types}},
url = {http://dx.doi.org/10.1021/ci00028a014},
doi = {10.1021/ci00028a014},
number = {6},
urldate = {2015-10-03},
journal = {Journal of Chemical Information and Computer Sciences},
author = {Hall, Lowell H. and Kier, Lemont B.},
month = nov,
year = {1995},
pages = {1039--1045},
file = {ACS Full Text PDF:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/FJUQDPXX/Hall と Kier - 1995 - Electrotopological State Indices for Atom Types A.pdf:application/pdf;ACS Full Text Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/DVC8EIB4/ci00028a014.html:text/html;Full Text PDF:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/GMTJZF3E/Hall と Kier - 1995 - Electrotopological State Indices for Atom Types A.pdf:application/pdf;Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/IUXZN9CC/ci00028a014.html:text/html}
}
% ExtendedTopochemicalAtom
@article{10.1021/ci0342066,
title = {{QSTR} with {Extended} {Topochemical} {Atom} {Indices}. 2. {Fish} {Toxicity} of {Substituted} {Benzenes}},
volume = {44},
issn = {0095-2338},
url = {http://dx.doi.org/10.1021/ci0342066},
doi = {10.1021/ci0342066},
abstract = {Considering the importance of quantitative structure-toxicity relationship (QSTR) studies in the field of aquatic toxicology from the viewpoint of ecological safety assessment, fish toxicity of various benzene derivatives has been modeled by the multiple regression technique using recently introduced extended topochemical atom (ETA) indices. The toxicity data have also been modeled using other selected topological descriptors and physicochemical variables, and the best ETA model has been compared to the non-ETA ones. Principal component factor analysis was used as the data preprocessing step to reduce the dimensionality of the data matrix and identify the important variables that are devoid of collinearities. All-possible-subsets regression was also applied on the parameters to cross-check the variable selection for the best model. Multiple linear regression analyses show that the best non-ETA model involves 1?, ALogP98, and LUMO (energy) as predictor variables and the quality of the relation is as follows:? n = 92, Q2 = 0.718, Ra2 = 0.730, R2 = 0.738, R = 0.859, F = 82.8 (df 3, 88), s = 0.340. On the other hand, the best ETA model has the following quality:? n = 92, Q2 = 0.865, Ra2 = 0.876, R2 = 0.885, R = 0.941, F = 92.6 (df 7, 84), s = 0.230. The ETA relations showed positive contributions of molecular bulk (size), chloro and hydroxy substitutions in the benzene ring, and the simultaneous presence of methyl and nitro substitutions to the toxicity. Further, the presence of fluoro and ether functionality, amino or nitro functionality in an otherwise unsubstituted ring, and nitro functionality that is ortho to a chloro substituent decreases toxicity. An attempt to use non-ETA descriptors along with ETA ones did not improve the quality in comparison to the best ETA model. Interestingly, the ETA model developed presently for the fish toxicity is better than the previously reported models on the same data set. Thus, it appears that ETA descriptors have significant potential in QSAR/QSPR/QSTR studies, which warrants extensive evaluation.},
number = {2},
urldate = {2015-10-03},
journal = {Journal of Chemical Information and Computer Sciences},
author = {Roy, Kunal and Ghosh, Gopinath},
month = mar,
year = {2004},
pages = {559--567},
file = {ACS Full Text PDF w/ Links:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/NNA8597X/Roy と Ghosh - 2004 - QSTR with Extended Topochemical Atom Indices. 2. F.pdf:application/pdf;ACS Full Text Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/UKD3MTA6/ci0342066.html:text/html}
}
@article{10.1016/j.jhazmat.2013.03.023,
title = {{QSTR} with extended topochemical atom ({ETA}) indices. 16. {Development} of predictive classification and regression models for toxicity of ionic liquids towards {Daphnia} magna},
volume = {254–255},
issn = {0304-3894},
url = {http://www.sciencedirect.com/science/article/pii/S0304389413001994},
doi = {10.1016/j.jhazmat.2013.03.023},
abstract = {Ionic liquids have been judged much with respect to their wide applicability than their considerable harmful effects towards the living ecosystem which has been observed in many instances. Hence, toxicological introspection of these chemicals by the development of predictive mathematical models can be of good help. This study presents an attempt to develop predictive classification and regression models correlating the structurally derived chemical information of a group of 62 diverse ionic liquids with their toxicity towards Daphnia magna and their interpretation. We have principally used the extended topochemical atom (ETA) indices along with various topological non-ETA and thermodynamic parameters as independent variables. The developed quantitative models have been subjected to extensive statistical tests employing multiple validation strategies from which acceptable results have been reported. The best models obtained from classification and regression studies captured necessary structural information on lipophilicity, branching pattern, electronegativity and chain length of the cationic substituents for explaining ecotoxicity of ionic liquids towards D. magna. The derived information can be successfully used to design better ionic liquid analogues acquiring the qualities of a true eco-friendly green chemical.},
urldate = {2016-01-21},
journal = {Journal of Hazardous Materials},
author = {Roy, Kunal and Das, Rudra Narayan},
month = jun,
year = {2013},
keywords = {Ecotoxicological hazard, ETA, Green chemistry, Ionic liquids, QSTR},
pages = {166--178},
file = {mmc1.doc:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/PQIN2DCX/mmc1.doc:application/msword;ScienceDirect Full Text PDF:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/FEIDFH34/Roy と Das - 2013 - QSTR with extended topochemical atom (ETA) indices.pdf:application/pdf;ScienceDirect Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/GATMM6S2/S0304389413001994.html:text/html}
}
% FragmentComplexity
@article{10.1021/ci050521b,
title = {A {Family} of {Ring} {System}-{Based} {Structural} {Fragments} for {Use} in {Structure}−{Activity} {Studies}: {Database} {Mining} and {Recursive} {Partitioning}},
volume = {46},
issn = {1549-9596},
shorttitle = {A {Family} of {Ring} {System}-{Based} {Structural} {Fragments} for {Use} in {Structure}−{Activity} {Studies}},
url = {http://dx.doi.org/10.1021/ci050521b},
doi = {10.1021/ci050521b},
abstract = {In earlier work from our laboratory, we have described the use of the ring system and ring scaffold as descriptors. We showed that these descriptors could be used for fast compound clustering, novelty determination, compound acquisition, and combinatorial library design. Here we extend the concept to a whole family of structural descriptors with the ring system as the centerpiece. We show how this simple idea can be used to build powerful search tools for mining chemical databases in useful ways. We have also built recursive partition trees using these fragments as descriptors. We will discuss how these trees can help in analyzing complex structure?activity data.},
number = {3},
urldate = {2015-10-03},
journal = {Journal of Chemical Information and Modeling},
author = {Nilakantan, Ramaswamy and Nunn, David S. and Greenblatt, Lynne and Walker, Gary and Haraki, Kevin and Mobilio, Dominick},
month = may,
year = {2006},
pages = {1069--1077},
file = {ACS Full Text PDF w/ Links:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/9UHBB27E/Nilakantan et al. - 2006 - A Family of Ring System-Based Structural Fragments.pdf:application/pdf;ACS Full Text PDF w/ Links:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/EWX9MCHI/Nilakantan et al. - 2006 - A Family of Ring System-Based Structural Fragments.pdf:application/pdf;ACS Full Text Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/5JMRSHVH/ci050521b.html:text/html;ACS Full Text Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/SM7ZJHQD/ci050521b.html:text/html}
}
% Framework
@article{10.1021/jm9602928,
title = {The {Properties} of {Known} {Drugs}. 1. {Molecular} {Frameworks}},
volume = {39},
issn = {0022-2623},
url = {http://dx.doi.org/10.1021/jm9602928},
doi = {10.1021/jm9602928},
abstract = {In order to better understand the common features present in drug molecules, we use shape description methods to analyze a database of commercially available drugs and prepare a list of common drug shapes. A useful way of organizing this structural data is to group the atoms of each drug molecule into ring, linker, framework, and side chain atoms. On the basis of the two-dimensional molecular structures (without regard to atom type, hybridization, and bond order), there are 1179 different frameworks among the 5120 compounds analyzed. However, the shapes of half of the drugs in the database are described by the 32 most frequently occurring frameworks. This suggests that the diversity of shapes in the set of known drugs is extremely low. In our second method of analysis, in which atom type, hybridization, and bond order are considered, more diversity is seen; there are 2506 different frameworks among the 5120 compounds in the database, and the most frequently occurring 42 frameworks account for only one-fourth of the drugs. We discuss the possible interpretations of these findings and the way they may be used to guide future drug discovery research.},
number = {15},
urldate = {2015-10-03},
journal = {Journal of Medicinal Chemistry},
author = {Bemis, Guy W. and Murcko, Mark A.},
month = jan,
year = {1996},
pages = {2887--2893},
file = {ACS Full Text PDF w/ Links:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/52WESTKU/Bemis と Murcko - 1996 - The Properties of Known Drugs. 1. Molecular Framew.pdf:application/pdf;ACS Full Text Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/3IKPWKXK/jm9602928.html:text/html}
}
% Property.McGowanVolume
@article{10.1007/BF02311772,
title = {The use of characteristic volumes to measure cavity terms in reversed phase liquid chromatography},
volume = {23},
issn = {0009-5893, 1612-1112},
url = {http://link.springer.com/article/10.1007/BF02311772},
doi = {10.1007/BF02311772},
language = {en},
number = {4},
urldate = {2015-10-03},
journal = {Chromatographia},
author = {Abraham, M. H. and McGowan, J. C.},
month = apr,
year = {1987},
keywords = {Analytical Chemistry, Biochemistry, general, Cavity term, Characteristic volumes, Liquid chromatography, Measurement Science, Instrumentation, Organic Chemistry, Pharmacy, Plant Sciences, Reversed-phase capacity factors},
pages = {243--246},
file = {Full Text PDF:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/TAJZEC38/Abraham と McGowan - 1987 - The use of characteristic volumes to measure cavit.pdf:application/pdf;Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/A645WXRD/10.html:text/html}
}
% Property.VdwVolumeABC
@article{10.1021/jo034808o,
title = {Fast {Calculation} of van der {Waals} {Volume} as a {Sum} of {Atomic} and {Bond} {Contributions} and {Its} {Application} to {Drug} {Compounds}},
volume = {68},
issn = {0022-3263},
url = {http://dx.doi.org/10.1021/jo034808o},
doi = {10.1021/jo034808o},
abstract = {The van der Waals volume is a widely used descriptor in modeling physicochemical properties. However, the calculation of the van der Waals volume (VvdW) is rather time-consuming, from Bondi group contributions, for a large data set. A new method for calculating van der Waals volume has been developed, based on Bondi radii. The method, termed Atomic and Bond Contributions of van der Waals volume (VABC), is very simple and fast. The only information needed for calculating VABC is atomic contributions and the number of atoms, bonds, and rings. Then, the van der Waals volume (Å3/molecule) can be calculated from the following formula:? VvdW = ??all atom??contributions ? 5.92NB ? 14.7RA ? 3.8RNR (NB is the number of bonds, RA is the number of aromatic rings, and RNA is the number of nonaromatic rings). The number of bonds present (NB) can be simply calculated by NB = N ? 1 + RA + RNA (where N is the total number of atoms). A simple Excel spread sheet has been made to calculate van der Waals volumes for a wide range of 677 organic compounds, including 237 drug compounds. The results show that the van der Waals volumes calculated from VABC are equivalent to the computer-calculated van der Waals volumes for organic compounds.},
number = {19},
urldate = {2015-10-06},
journal = {The Journal of Organic Chemistry},
author = {Zhao, Yuan H. and Abraham, Michael H. and Zissimos, Andreas M.},
month = sep,
year = {2003},
pages = {7368--7373},
file = {ACS Full Text PDF w/ Links:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/PAKZ8AGR/Zhao et al. - 2003 - Fast Calculation of van der Waals Volume as a Sum .pdf:application/pdf;ACS Full Text Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/4D3MMWPG/jo034808o.html:text/html;jo034808osi20030611_100954.xls:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/RH924VVE/jo034808osi20030611_100954.xls:application/vnd.ms-excel}
}
% Property.WildmanCrippenLogP
@article{10.1021/ci990307l,
title = {Prediction of {Physicochemical} {Parameters} by {Atomic} {Contributions}},
volume = {39},
issn = {0095-2338},
url = {http://dx.doi.org/10.1021/ci990307l},
doi = {10.1021/ci990307l},
abstract = {We present a new atom type classification system for use in atom-based calculation of partition coefficient (log P) and molar refractivity (MR) designed in part to address published concerns of previous atomic methods. The 68 atomic contributions to log P have been determined by fitting an extensive training set of 9920 molecules, with r2 = 0.918 and σ = 0.677. A separate set of 3412 molecules was used for the determination of contributions to MR with r2 = 0.997 and σ = 1.43. Both calculations are shown to have high predictive ability.},
number = {5},
urldate = {2015-10-03},
journal = {Journal of Chemical Information and Computer Sciences},
author = {Wildman, Scott A. and Crippen, Gordon M.},
month = sep,
year = {1999},
pages = {868--873},
file = {ACS Full Text PDF w/ Links:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/WI4FKBNP/Wildman と Crippen - 1999 - Prediction of Physicochemical Parameters by Atomic.pdf:application/pdf;ACS Full Text Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/B52V673M/ci990307l.html:text/html}
}
% TPSA
@article{10.1021/jm000942e,
title = {Fast {Calculation} of {Molecular} {Polar} {Surface} {Area} as a {Sum} of {Fragment}-{Based} {Contributions} and {Its} {Application} to the {Prediction} of {Drug} {Transport} {Properties}},
volume = {43},
issn = {0022-2623},
url = {http://dx.doi.org/10.1021/jm000942e},
doi = {10.1021/jm000942e},
abstract = {Molecular polar surface area (PSA), i.e., surface belonging to polar atoms, is a descriptor that was shown to correlate well with passive molecular transport through membranes and, therefore, allows prediction of transport properties of drugs. The calculation of PSA, however, is rather time-consuming because of the necessity to generate a reasonable 3D molecular geometry and the calculation of the surface itself. A new approach for the calculation of the PSA is presented here, based on the summation of tabulated surface contributions of polar fragments. The method, termed topological PSA (TPSA), provides results which are practically identical with the 3D PSA (the correlation coefficient between 3D PSA and fragment-based TPSA for 34?810 molecules from the World Drug Index is 0.99), while the computation speed is 2?3 orders of magnitude faster. The new methodology may, therefore, be used for fast bioavailability screening of virtual libraries having millions of molecules. This article describes the new methodology and shows the results of validation studies based on sets of published absorption data, including intestinal absorption, Caco-2 monolayer penetration, and blood?brain barrier penetration.},
number = {20},
urldate = {2015-10-06},
journal = {Journal of Medicinal Chemistry},
author = {Ertl, Peter and Rohde, Bernhard and Selzer, Paul},
month = oct,
year = {2000},
pages = {3714--3717},
file = {ACS Full Text PDF w/ Links:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/BPKC7I8A/Ertl et al. - 2000 - Fast Calculation of Molecular Polar Surface Area a.pdf:application/pdf;ACS Full Text Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/FV667RQU/jm000942e.html:text/html}
}
% TopologicalCharge
@article{10.1021/ci00019a008,
title = {Charge {Indexes}. {New} {Topological} {Descriptors}},
volume = {34},
issn = {0095-2338},
url = {http://dx.doi.org/10.1021/ci00019a008},
doi = {10.1021/ci00019a008},
number = {3},
urldate = {2015-10-09},
journal = {Journal of Chemical Information and Computer Sciences},
author = {Galvez, J. and Garcia, R. and Salabert, M. T. and Soler, R.},
month = may,
year = {1994},
pages = {520--525},
file = {ACS Full Text PDF:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/QRPK4SE2/Galvez et al. - 1994 - Charge Indexes. New Topological Descriptors.pdf:application/pdf;ACS Full Text Snapshot:/Users/philopon/Library/Application Support/Firefox/Profiles/q8kekyxs.default/zotero/storage/VZGV48UG/ci00019a008.html:text/html}
}