当前位置： SCI文献检索 > Journal of Chemical Information and Modeling期刊下所有文献 > Determining the validity of a QSAR model--a classification approach.

Determining the validity of a QSAR model--a classification approach.

Abstract：

:The determination of the validity of a QSAR model when applied to new compounds is an important concern in the field of QSAR and QSPR modeling. Various scoring techniques can be applied to specific types of models. We present a technique with which we can state whether a new compound will be well predicted by a previously built QSAR model. In this study we focus on linear regression models only, though the technique is general and could also be applied to other types of quantitative models. Our technique is based on a classification method that divides regression residuals from a previously generated model into a good class and bad class and then builds a classifier based on this division. The trained classifier is then used to determine the class of the residual for a new compound. We investigated the performance of a variety of classifiers, both linear and nonlinear. The technique was tested on two data sets from the literature and a hand built data set. The data sets selected covered both physical and biological properties and also presented the methodology with quantitative regression models of varying quality. The results indicate that this technique can determine whether a new compound will be well or poorly predicted with weighted success rates ranging from 73% to 94% for the best classifier.

journal_name

J Chem Inf Model

journal_title

Journal of chemical information and modeling

authors

Guha R,Jurs PC

doi

10.1021/ci0497511

keywords:

subject

Has Abstract

pub_date

2005-01-01 00:00:00

pages

65-73

issue

1

eissn

1549-9596

issn

1549-960X

journal_volume

45

pub_type

杂志文章

相关文献

Journal of Chemical Information and Modeling文献大全
  • Ligand-based molecular modeling study on a chemically diverse series of cholecystokinin-B/gastrin receptor antagonists: generation of predictive model.

    abstract：:Pharmacophore hypotheses were developed for six structurally diverse series of cholecystokinin-B/gastrin receptor (CCK-BR) antagonists. A training set consisting of 33 compounds was carefully selected. The activity spread of the training set molecules was from 0.1 to 2100 nM. The most predictive pharmacophore model (h...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci050257m

    authors： Chopra M,Mishra AK

    更新日期：2005-11-01 00:00:00

  • Informatics-Aided Density Functional Theory Study on the Li Ion Transport of Tavorite-Type LiMTO4F (M(3+)-T(5+), M(2+)-T(6+)).

    abstract：:The ongoing search for fast Li-ion conducting solid electrolytes has driven the deployment surge on density functional theory (DFT) computation and materials informatics for exploring novel chemistries before actual experimental testing. Existing structure prototypes can now be readily evaluated beforehand not only to...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci500752n

    authors： Jalem R,Kimura M,Nakayama M,Kasuga T

    更新日期：2015-06-22 00:00:00

  • Phosphorylation of Fibronectin Influences the Structural Stability of the Predicted Interchain Domain.

    abstract：:As a key player in cell adhesion, the glycoprotein fibronectin is involved in the complex mechanobiology of the extracellular matrix. Although the function of many modules in the fibronectin molecule has already been understood, the structure and biological relevance of the C-terminal cross-linked region (CTXL) still ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00555

    authors： Kulke M,Uhrhan M,Geist N,Brüggemann D,Ohler B,Langel W,Köppen S

    更新日期：2019-10-28 00:00:00

  • Searching for coordinated activity cliffs using particle swarm optimization.

    abstract：:Activity cliffs are formed by structurally similar compounds having large potency differences. Coordinated activity cliffs evolve when compounds within groups of structural neighbors form multiple cliffs with different partners, giving rise to local networks of cliffs in a data set. Using particle swarm optimization, ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci3000503

    authors： Namasivayam V,Bajorath J

    更新日期：2012-04-23 00:00:00

  • Multiple e-pharmacophore modeling, 3D-QSAR, and high-throughput virtual screening of hepatitis C virus NS5B polymerase inhibitors.

    abstract：:The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRP) is a crucial and unique component of the HCV RNA replication machinery and a validated target for drug discovery. Multiple crystal structures of NS5B inhibitor complexes have facilitated the identification of novel compound scaffolds through in silic...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci400644r

    authors： Therese PJ,Manvar D,Kondepudi S,Battu MB,Sriram D,Basu A,Yogeeswari P,Kaushik-Basu N

    更新日期：2014-02-24 00:00:00

  • CRDOCK: an ultrafast multipurpose protein-ligand docking tool.

    abstract：:An ultrafast docking and virtual screening program, CRDOCK, is presented that contains (1) a search engine that can use a variety of sampling methods and an initial energy evaluation function, (2) several energy minimization algorithms for fine tuning the binding poses, and (3) different scoring functions. This modula...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci300194a

    authors： Cortés Cabrera Á,Klett J,Dos Santos HG,Perona A,Gil-Redondo R,Francis SM,Priego EM,Gago F,Morreale A

    更新日期：2012-08-27 00:00:00

  • Conformator: A Novel Method for the Generation of Conformer Ensembles.

    abstract：:Computer-aided drug design methods such as docking, pharmacophore searching, 3D database searching, and the creation of 3D-QSAR models need conformational ensembles to handle the flexibility of small molecules. Here, we present Conformator, an accurate and effective knowledge-based algorithm for generating conformer e...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.8b00704

    authors： Friedrich NO,Flachsenberg F,Meyder A,Sommer K,Kirchmair J,Rarey M

    更新日期：2019-02-25 00:00:00

  • In silico deconstruction of ATP-competitive inhibitors of glycogen synthase kinase-3β.

    abstract：:Fragment-based methods have emerged in the last two decades as alternatives to traditional high throughput screenings for the identification of chemical starting points in drug discovery. One arguable yet popular assumption about fragment-based design is that the fragment binding mode remains conserved upon chemical e...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci300355p

    authors： Bisignano P,Lambruschini C,Bicego M,Murino V,Favia AD,Cavalli A

    更新日期：2012-12-21 00:00:00

  • Enrichment factor analyses on G-protein coupled receptors with known crystal structure.

    abstract：:G-protein coupled receptors (GPCRs) are highly relevant drug targets. Four GPCRs with known crystal structure were analyzed with docking (AutoDock4) and postdocking (MM-PBSA) in order to evaluate the ability to recognize known antagonists from a larger database of molecular decoys and to predict correct binding modes....

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci4000745

    authors： Anighoro A,Rastelli G

    更新日期：2013-04-22 00:00:00

  • Isomerization and Decomposition of 2-Methylfuran with External Forces.

    abstract：:The primary goal of this project was to evaluate the performance of the Standard and Enforced Geometry Optimization (SEGO) method which we have recently developed. The SEGO method has been designed for an automatic location of multiple minima on the molecular Potential Energy Surface (PES), and its usefulness has been...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00352

    authors： Brzyska A,Woliński K

    更新日期：2019-08-26 00:00:00

  • Allosteric Response of DNA Recognition Helices of Catabolite Activator Protein to cAMP and DNA Binding.

    abstract：:The homodimeric catabolite activator protein (CAP) regulates the transcription of several bacterial genes based on the cellular concentration of cyclic adenosine monophosphate (cAMP). The binding of cAMP to CAP triggers allosteric communication between the cAMP binding domains (CBD) and DNA binding domains (DBD) of CA...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00617

    authors： Prabhakant A,Panigrahi A,Krishnan M

    更新日期：2020-12-28 00:00:00

  • Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: predicting affinity and conformational sampling.

    abstract：:Cytochrome P450 2D6 (CYP2D6) is used to develop an approach for predicting affinity and relevant binding conformation(s) for highly flexible binding sites. The approach combines the use of docking scores and compound properties as attributes in building a neural network (NN) model. It begins by identifying segments of...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci600267k

    authors： Bazeley PS,Prithivi S,Struble CA,Povinelli RJ,Sem DS

    更新日期：2006-11-01 00:00:00

  • Similarity perception of reactions catalyzed by oxidoreductases and hydrolases using different classification methods.

    abstract：:In this work, the perception of similarity of reactions catalyzed by hydrolases and oxidoreductases on the basis of the overall breaking and making of bonds of reactions is investigated. Six physicochemical properties for the reacting bond in the substrate of each enzymatic reaction were calculated to describe the cha...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci9004833

    authors： Hu X,Yan A,Tan T,Sacher O,Gasteiger J

    更新日期：2010-06-28 00:00:00

  • CoMFA, CoMSIA, and molecular hologram QSAR studies of novel neuronal nAChRs ligands-open ring analogues of 3-pyridyl ether.

    abstract：:3-Pyridyl ethers are excellent nAChRs ligands, which show high subtype selectivity and binding affinity to alpha4beta2 nAChR. Although the quantitative structure-activity relationship (QSAR) of nAChRs ligands has been widely investigated using various classes of compounds, the open ring analogues of 3-pyridyl ethers h...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci0498113

    authors： Zhang H,Li H,Liu C

    更新日期：2005-03-01 00:00:00

  • Structural protein-ligand interaction fingerprints (SPLIF) for structure-based virtual screening: method and benchmark study.

    abstract：:Accurate and affordable assessment of ligand-protein affinity for structure-based virtual screening (SB-VS) is a standing challenge. Hence, empirical postdocking filters making use of various types of structure-activity information may prove useful. Here, we introduce one such filter based upon three-dimensional struc...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci500319f

    authors： Da C,Kireev D

    更新日期：2014-09-22 00:00:00

  • Effect of input differences on the results of docking calculations.

    abstract：:The sensitivity of docking calculations to the geometry of the input ligand was studied. It was found that even small changes in the ligand input conformation can lead to large differences in the geometries and scores of the resulting docked poses. The accuracy of docked poses produced from different ligand input stru...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci9000629

    authors： Feher M,Williams CI

    更新日期：2009-07-01 00:00:00

  • Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures.

    abstract：:To discover non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) that are effective against both wild-type (WT) virus and variants that encode the clinically troublesome Tyr181Cys (Y181C) RT mutation, virtual screening by docking was carried out using three RT structures and more than 2 million commercial...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci900068k

    authors： Nichols SE,Domaoal RA,Thakur VV,Tirado-Rives J,Anderson KS,Jorgensen WL

    更新日期：2009-05-01 00:00:00

  • Molecular Self-Assembly Strategy for Encapsulation of an Amphipathic α-Helical Antimicrobial Peptide into the Different Polymeric and Copolymeric Nanoparticles.

    abstract：:Encapsulation of peptide and protein-based drugs in polymeric nanoparticles is one of the fundamental fields in controlled-release drug delivery systems. The molecular mechanisms of absorption of peptides to the polymeric nanoparticles are still unknown, and there is no precise molecular data on the encapsulation proc...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.8b00641

    authors： Jafari M,Doustdar F,Mehrnejad F

    更新日期：2019-01-28 00:00:00

  • Flux (2): comparison of molecular mutation and crossover operators for ligand-based de novo design.

    abstract：:We implemented a fragment-based de novo design algorithm for a population-based optimization of molecular structures. The concept is grounded on an evolution strategy with mutation and crossover operators for structure breeding. Molecular building blocks were obtained from the pseudo-retrosynthesis of a collection of ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci6005307

    authors： Fechner U,Schneider G

    更新日期：2007-03-01 00:00:00

  • Customizable Generation of Synthetically Accessible, Local Chemical Subspaces.

    abstract：:Screening large libraries of chemicals has been an efficient strategy to discover bioactive compounds; however a portion of the potential for success is limited to the available libraries. Synergizing combinatorial and computational chemistries has emerged as a time-efficient strategy to explore the chemical space mor...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.6b00648

    authors： Pottel J,Moitessier N

    更新日期：2017-03-27 00:00:00

  • FORTRAN interface for code interoperability in quantum chemistry: the Q5Cost library.

    abstract：:Ab initio quantum-chemistry programs produce and use large amounts of data, which are usually stored on disk in the form of binary files. A FORTRAN library, named Q5Cost, has been designed and implemented in order to allow the storage of these data sets in a special data format built with the HDF5 technology. This dat...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci7000567

    authors： Borini S,Monari A,Rossi E,Tajti A,Angeli C,Bendazzoli GL,Cimiraglia R,Emerson A,Evangelisti S,Maynau D,Sanchez-Marin J,Szalay PG

    更新日期：2007-05-01 00:00:00

  • Searching for New Leads To Treat Epilepsy: Target-Based Virtual Screening for the Discovery of Anticonvulsant Agents.

    abstract：:The purpose of this investigation is to contribute to the development of new anticonvulsant drugs to treat patients with refractory epilepsy. We applied a virtual screening protocol that involved the search into molecular databases of new compounds and known drugs to find small molecules that interact with the open co...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.7b00721

    authors： Palestro PH,Enrique N,Goicoechea S,Villalba ML,Sabatier LL,Martin P,Milesi V,Bruno Blanch LE,Gavernet L

    更新日期：2018-07-23 00:00:00

  • Consensus adaptation of fields for molecular comparison (AFMoC) models incorporate ligand and receptor conformational variability into tailor-made scoring functions.

    abstract：:Taking into account dynamical behavior and/or structural inaccuracies of receptor-ligand systems becomes increasingly important in structure-based drug design. Here, we describe the development of consensus Adaptation of Fields for Molecular Comparison (AFMoC) (abbreviated as AFMoCcon) models that account for multiple...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci7002472

    authors： Breu B,Silber K,Gohlke H

    更新日期：2007-11-01 00:00:00

  • Transplant-insert-constrain-relax-assemble (TICRA): protein-ligand complex structure modeling and application to kinases.

    abstract：:We introduce TICRA (transplant-insert-constrain-relax-assemble), a method for modeling the structure of unknown protein-ligand complexes using the X-ray crystal structures of homologous proteins and ligands with known activity. We present results from modeling the structures of protein kinase-inhibitor complexes using...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci100256u

    authors： Meshkat S,Klon AE,Zou J,Wiseman JS,Konteatis Z

    更新日期：2011-01-24 00:00:00

  • Concept-based semi-automatic classification of drugs.

    abstract：:The anatomical therapeutic chemical (ATC) classification system maintained by the World Health Organization provides a global standard for the classification of medical substances and serves as a source for drug repurposing research. Nevertheless, it lacks several drugs that are major players in the global drug market...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci9000844

    authors： Gurulingappa H,Kolárik C,Hofmann-Apitius M,Fluck J

    更新日期：2009-08-01 00:00:00

  • Evaluation of different virtual screening programs for docking in a charged binding pocket.

    abstract：:Virtual screening of small molecules against a protein target often identifies the correct pose, but the ranking in terms of binding energy remains a difficult problem, resulting in unacceptable numbers of false positives and negatives. To investigate this problem, the performance of three docking programs, FRED, QXP/...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci800154w

    authors： Deng W,Verlinde CL

    更新日期：2008-10-01 00:00:00

  • Posetic quantitative superstructure/activity relationships (QSSARs) for chlorobenzenes.

    abstract：:As a result of the widespread industrial use of polychlorinated hydrocarbons, they have accumulated in nearly all types of environmental compartments, especially in aquatic systems. Particularly, chloroaromatics are among the most undesirable industrial effluents because of their persistence and toxicity. To predict c...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci0501342

    authors： Ivanciuc T,Ivanciuc O,Klein DJ

    更新日期：2005-07-01 00:00:00

  • Baseline Model for Predicting Protein-Ligand Unbinding Kinetics through Machine Learning.

    abstract：:Derivation of structure-kinetics relationships can help rational design and development of new small-molecule drug candidates with desired residence times. Efforts are now being directed toward the development of efficient computational methods. Currently, there is a lack of solid, high-throughput binding kinetics pre...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00450

    authors： Amangeldiuly N,Karlov D,Fedorov MV

    更新日期：2020-12-28 00:00:00

  • Predicted Biological Activity of Purchasable Chemical Space.

    abstract：:Whereas 400 million distinct compounds are now purchasable within the span of a few weeks, the biological activities of most are unknown. To facilitate access to new chemistry for biology, we have combined the Similarity Ensemble Approach (SEA) with the maximum Tanimoto similarity to the nearest bioactive to predict a...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.7b00316

    authors： Irwin JJ,Gaskins G,Sterling T,Mysinger MM,Keiser MJ

    更新日期：2018-01-22 00:00:00

  • Probabilistic models for capturing more physicochemical properties on protein-protein interface.

    abstract：:Protein-protein interactions play a key role in a multitude of biological processes, such as signal transduction, de novo drug design, immune responses, and enzymatic activities. It is of great interest to understand how proteins interact with each other. The general approach is to explore all possible poses and ident...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci5002372

    authors： Guo F,Li SC,Du P,Wang L

    更新日期：2014-06-23 00:00:00