当前位置： SCI文献检索 > Journal of Chemical Information and Modeling期刊下所有文献 > New fragment weighting scheme for the Bayesian inference network in ligand-based virtual screening.

New fragment weighting scheme for the Bayesian inference network in ligand-based virtual screening.

Abstract：

:Many of the conventional similarity methods assume that molecular fragments that do not relate to biological activity carry the same weight as the important ones. One possible approach to this problem is to use the Bayesian inference network (BIN), which models molecules and reference structures as probabilistic inference networks. The relationships between molecules and reference structures in the Bayesian network are encoded using a set of conditional probability distributions, which can be estimated by the fragment weighting function, a function of the frequencies of the fragments in the molecule or the reference structure as well as throughout the collection. The weighting function combines one or more fragment weighting schemes. In this paper, we have investigated five different weighting functions and present a new fragment weighting scheme. Later on, these functions were modified to combine the new weighting scheme. Simulated virtual screening experiments with the MDL Drug Data Report (23) and maximum unbiased validation data sets show that the use of new weighting scheme can provide significantly more effective screening when compared with the use of current weighting schemes.

journal_name

J Chem Inf Model

journal_title

Journal of chemical information and modeling

authors

Abdo A,Salim N

doi

10.1021/ci100232h

subject

Has Abstract

pub_date

2011-01-24 00:00:00

pages

25-32

issue

1

eissn

1549-9596

issn

1549-960X

journal_volume

51

pub_type

杂志文章

相关文献

Journal of Chemical Information and Modeling文献大全
  • Molecular Modeling Investigation of the Interaction between Humicola insolens Cutinase and SDS Surfactant Suggests a Mechanism for Enzyme Inactivation.

    abstract：:One of the largest commercial applications of enzymes and surfactants is as main components in modern detergents. The high concentration of surfactant compounds usually present in detergents can, however, negatively affect the enzymatic activity. To remedy this drawback, it is of great importance to characterize the i...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.8b00857

    authors： Kjølbye LR,Laustsen A,Vestergaard M,Periole X,De Maria L,Svendsen A,Coletta A,Schiøtt B

    更新日期：2019-05-28 00:00:00

  • Standardizing and simplifying analysis of peptide library data.

    abstract：:Peptide libraries allow researchers to quickly find hundreds of peptide sequences with a desired property. Currently, the large amount of data generated from peptide libraries is analyzed by hand, where researchers search for repeating patterns in the peptide sequences. Such patterns are called motifs. In this work, w...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci300484q

    authors： White AD,Keefe AJ,Nowinski AK,Shao Q,Caldwell K,Jiang S

    更新日期：2013-02-25 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

  • Efficient Corrections for DFT Noncovalent Interactions Based on Ensemble Learning Models.

    abstract：:Machine learning has exhibited powerful capabilities in many areas. However, machine learning models are mostly database dependent, requiring a new model if the database changes. Therefore, a universal model is highly desired to accommodate the widest variety of databases. Fortunately, this universality may be achieve...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.8b00878

    authors： Li W,Miao W,Cui J,Fang C,Su S,Li H,Hu L,Lu Y,Chen G

    更新日期：2019-05-28 00:00:00

  • Stability studies of transition-metal linkage isomers using quantum mechanical methods. Groups 11 and 12 transition metals.

    abstract：:Several hypotheses to elucidate the linkage isomer preference of the thiocyanate (SCN(-)) ion have been offered. For complexes with small coordination numbers (i.e., 1 and 2) and groups 11 (Cu-triad) and 12 (Zn-triad) metals, different levels of theory and a variety of basis sets have been employed to study linkage is...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci050050t

    authors： Buda C,Kazi AB,Dinescu A,Cundari TR

    更新日期：2005-07-01 00:00:00

  • Real external predictivity of QSAR models. Part 2. New intercomparable thresholds for different validation criteria and the need for scatter plot inspection.

    abstract：:The evaluation of regression QSAR model performance, in fitting, robustness, and external prediction, is of pivotal importance. Over the past decade, different external validation parameters have been proposed: Q(F1)(2), Q(F2)(2), Q(F3)(2), r(m)(2), and the Golbraikh-Tropsha method. Recently, the concordance correlati...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci300084j

    authors： Chirico N,Gramatica P

    更新日期：2012-08-27 00:00:00

  • T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex.

    abstract：:The recognition of peptide/MHC by T-cell receptors is one of the most important interactions in the adaptive immune system. A large number of computational studies have investigated the structural dynamics of this interaction. However, to date only limited attention has been paid to differences between the dynamics of...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.5b00511

    authors： Knapp B,Deane CM

    更新日期：2016-01-25 00:00:00

  • Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles.

    abstract：:Molecular docking can account for receptor flexibility by combining the docking score over multiple rigid receptor conformations, such as snapshots from a molecular dynamics simulation. Here, we evaluate a number of common snapshot selection strategies using a quality metric from stratified sampling, the efficiency of...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.8b00314

    authors： Xie B,Clark JD,Minh DDL

    更新日期：2018-09-24 00:00:00

  • Including explicit water molecules as part of the protein structure in MM/PBSA calculations.

    abstract：:Water is the natural medium of molecules in the cell and plays an important role in protein structure, function and interaction with small molecule ligands. However, the widely used molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method for binding energy calculation does not explicitly take account of wa...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci4001794

    authors： Zhu YL,Beroza P,Artis DR

    更新日期：2014-02-24 00:00:00

  • Allosteric Modulation of Human Hsp90α Conformational Dynamics.

    abstract：:Central to Hsp90's biological function is its ability to interconvert between various conformational states. Drug targeting of Hsp90's regulatory mechanisms, including its modulation by cochaperone association, presents as an attractive therapeutic strategy for Hsp90 associated pathologies. In this study, we utilized ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.7b00630

    authors： Penkler DL,Atilgan C,Tastan Bishop Ö

    更新日期：2018-02-26 00:00:00

  • Pharmacophore identification, in silico screening, and virtual library design for inhibitors of the human factor Xa.

    abstract：:Factor Xa inhibitors are innovative anticoagulant agents that provide a better safety/efficacy profile compared to other anticoagulative drugs. A chemical feature-based modeling approach was applied to identify crucial pharmacophore patterns from 3D crystal structures of inhibitors bound to human factor Xa (Pdb entrie...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci049778k

    authors： Krovat EM,Frühwirth KH,Langer T

    更新日期：2005-01-01 00:00:00

  • Energetics, Thermodynamics, and Molecular Recognition of Piperine with DNA.

    abstract：:Piperine, the bioactive phytochemical from black pepper (Piper nigrum L.), is a nontoxic natural compound exhibiting many physiological and pharmacological properties. They include antioxidant, anti-inflammatory, antimutagenic, antitumor, antiapoptotic, antigenotoxic, antiarthritic, antifungal, antimicrobial, antidepr...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.5b00514

    authors： Haris P,Mary V,Haridas M,Sudarsanakumar C

    更新日期：2015-12-28 00:00:00

  • In silico target predictions: defining a benchmarking data set and comparison of performance of the multiclass Naïve Bayes and Parzen-Rosenblatt window.

    abstract：:In this study, two probabilistic machine-learning algorithms were compared for in silico target prediction of bioactive molecules, namely the well-established Laplacian-modified Naïve Bayes classifier (NB) and the more recently introduced (to Cheminformatics) Parzen-Rosenblatt Window. Both classifiers were trained in ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci300435j

    authors： Koutsoukas A,Lowe R,Kalantarmotamedi Y,Mussa HY,Klaffke W,Mitchell JB,Glen RC,Bender A

    更新日期：2013-08-26 00:00:00

  • Partitioning of pi-electrons in rings for Clar structures of benzenoid hydrocarbons.

    abstract：:Resonance structures of polycyclic aromatic hydrocarbons can be associated with numerical formulas by assigning pi-electrons of C=C double bonds to individual benzenoid rings. Each C=C double bond in a resonance structure assigns two pi-electrons to a ring in a fused-benzenoid system if it is not shared by adjacent ri...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci050196s

    authors： Randić M,Balaban AT

    更新日期：2006-01-01 00:00:00

  • Improved Scaffold Hopping in Ligand-Based Virtual Screening Using Neural Representation Learning.

    abstract：:Deep learning has demonstrated significant potential in advancing state of the art in many problem domains, especially those benefiting from automated feature extraction. Yet, the methodology has seen limited adoption in the field of ligand-based virtual screening (LBVS) as traditional approaches typically require lar...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00622

    authors： Stojanović L,Popović M,Tijanić N,Rakočević G,Kalinić M

    更新日期：2020-10-26 00:00:00

  • Physicochemical stereodescriptors of atomic chiral centers.

    abstract：:Physicochemical atomic stereodescriptors (PAS) were implemented that represent the chirality of an atomic chiral center on the basis of empirical physicochemical properties of the ligands. The ligands are ranked according to a specific property, and the chiral center takes an S/R-like descriptor relative to that prope...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci600235w

    authors： Zhang QY,Aires-de-Sousa J

    更新日期：2006-11-01 00:00:00

  • Comparison Study of Polar and Nonpolar Contributions to Solvation Free Energy.

    abstract：:In this study, we compared the contributions of polar and nonpolar interactions to the solvation free energy of a solute in solvent, which is decomposed into four different terms based on the nature of interactions: (i) electrostatic solvation free energy term counting for the work done to move solute charges from fix...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.7b00368

    authors： Izairi R,Kamberaj H

    更新日期：2017-10-23 00:00:00

  • Advantages of Relative versus Absolute Data for the Development of Quantitative Structure-Activity Relationship Classification Models.

    abstract：:The appropriate selection of a chemical space represented by the data set, the selection of its chemical data representation, the development of a correct modeling process using a robust and reproducible algorithm, and the performance of an exhaustive training and external validation determine the usability and reprod...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.7b00492

    authors： Ruiz IL,Gómez-Nieto MÁ

    更新日期：2017-11-27 00:00:00

  • Ab Initio Investigation of CO2 Adsorption on 13-Atom 4d Clusters.

    abstract：:In this work, we report an ab initio investigation based on density functional theory calculations within van der Waals D3 corrections to investigate the adsorption properties and activation of CO2 on transition-metal (TM) 13-atom clusters (TM = Ru, Rh, Pd, Ag), which is a key step for the development of subnano catal...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00792

    authors： Batista KEA,Ocampo-Restrepo VK,Soares MD,Quiles MG,Piotrowski MJ,Da Silva JLF

    更新日期：2020-02-24 00:00:00

  • Combined approach using ligand efficiency, cross-docking, and antitarget hits for wild-type and drug-resistant Y181C HIV-1 reverse transcriptase.

    abstract：:New hits against HIV-1 wild-type and Y181C drug-resistant reverse transcriptases were predicted taking into account the possibility of some of the known metabolism interactions. In silico hits against a set of antitargets (i.e., proteins or nucleic acids that are off-targets from the desired pharmaceutical target obje...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci200203h

    authors： García-Sosa AT,Sild S,Takkis K,Maran U

    更新日期：2011-10-24 00:00:00

  • Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets.

    abstract：:On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, a...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.5b00143

    authors： Clark AM,Dole K,Coulon-Spektor A,McNutt A,Grass G,Freundlich JS,Reynolds RC,Ekins S

    更新日期：2015-06-22 00:00:00

  • Computational fragment-based approach at PDB scale by protein local similarity.

    abstract：:The large volume of protein-ligand structures now available enables innovative and efficient protocols in computational FBDD (Fragment-Based Drug Design) to be proposed based on experimental data. In this work, we build a database of MED-Portions, where a MED-Portion is a new structural object encoding protein-fragmen...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci8003094

    authors： Moriaud F,Doppelt-Azeroual O,Martin L,Oguievetskaia K,Koch K,Vorotyntsev A,Adcock SA,Delfaud F

    更新日期：2009-02-01 00:00:00

  • Simulation-Based Algorithm for Two-Dimensional Chemical Structure Diagram Generation of Complex Molecules and Ligand-Protein Interactions.

    abstract：:Computer programs for structure diagram generation (SDG) are indispensable cheminformatic tools that translate one- or three-dimensional (1D or 3D) chemical structure data stored in electronic formats to human-readable 2D depictions. Although many such programs are known, only a moderate part of chemical space can be ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.6b00391

    authors： Frączek T

    更新日期：2016-12-27 00:00:00

  • Unraveling Energy and Dynamics Determinants to Interpret Protein Functional Plasticity: The Limonene-1,2-epoxide-hydrolase Case Study.

    abstract：:The balance between structural stability and functional plasticity in proteins that share common three-dimensional folds is the key factor that drives protein evolvability. The ability to distinguish the parts of homologous proteins that underlie common structural organization patterns from the parts acting as regulat...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.6b00504

    authors： Rinaldi S,Gori A,Annovazzi C,Ferrandi EE,Monti D,Colombo G

    更新日期：2017-04-24 00:00:00

  • Metabotropic glutamate receptor-mediated currents at the climbing fiber to Purkinje cell synapse.

    abstract：:Different forms of synaptic plasticity in the cerebellum expressed at the synapses onto Purkinje cells (PCs) are mediated by membrane metabotropic glutamate receptors (mGluRs). There are three main mGluR groups with a total of 8 subtypes. Although mGluRs are also found at the climbing fiber (CF) to PC synapses, the di...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci050161s

    authors： Andjus PR,Bajić A,Zhu L,Strata P

    更新日期：2005-11-01 00:00:00

  • Computational simulations of the interactions between acetyl-coenzyme-A carboxylase and clodinafop: resistance mechanism due to active and nonactive site mutations.

    abstract：:Grass weed populations resistant to acetyl-CoA carboxylase-inhibiting (ACCase; EC 6.4.1.2) herbicides represent a major problem for the sustainable development of modern agriculture. In the present study, extensive computational simulations, including homology modeling, molecular dynamics (MD) simulations, and molecul...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci900174d

    authors： Zhu XL,Ge-Fei H,Zhan CG,Yang GF

    更新日期：2009-08-01 00:00:00

  • Tautomer Standardization in Chemical Databases: Deriving Business Rules from Quantum Chemistry.

    abstract：:Databases of small, potentially bioactive molecules are ubiquitous across the industry and academia. Designed such that each unique compound should appear only once, the multiplicity of ways in which many compounds can be represented means that these databases require methods for standardizing the representation of ch...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00232

    authors： Baker CM,Kidley NJ,Papachristos K,Hotson M,Carson R,Gravestock D,Pouliot M,Harrison J,Dowling A

    更新日期：2020-08-24 00:00:00

  • Assessing different classification methods for virtual screening.

    abstract：:How well do different classification methods perform in selecting the ligands of a protein target out of large compound collections not used to train the model? Support vector machines, random forest, artificial neural networks, k-nearest-neighbor classification with genetic-algorithm-optimized feature selection, tren...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci050519k

    authors： Plewczynski D,Spieser SA,Koch U

    更新日期：2006-05-01 00:00:00

  • Accurate Hit Estimation for Iterative Screening Using Venn-ABERS Predictors.

    abstract：:Iterative screening has emerged as a promising approach to increase the efficiency of high-throughput screening (HTS) campaigns in drug discovery. By learning from a subset of the compound library, inferences on what compounds to screen next can be made by predictive models. One of the challenges of iterative screenin...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.8b00724

    authors： Buendia R,Kogej T,Engkvist O,Carlsson L,Linusson H,Johansson U,Toccaceli P,Ahlberg E

    更新日期：2019-03-25 00:00:00

  • BFMP: a method for discretizing and visualizing pyranose conformations.

    abstract：:We report a new classification method for pyranose ring conformations called Best-fit, Four-Membered Plane (BFMP), which describes pyranose ring conformations based on reference planes defined by four atoms. The method is able to characterize all asymmetrical and symmetrical shapes of a pyran ring, is readily automate...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci500325b

    authors： Makeneni S,Foley BL,Woods RJ

    更新日期：2014-10-27 00:00:00