Benchmark performance of MultiCASE Inc. software in Ames mutagenicity set.

abstract：:An in silico screening procedure was performed to select new inhibitors of glycogen synthase kinase 3β (GSK-3β), a serine/threonine protein kinase that in the last two decades has emerged as a key target in drug discovery, having been implicated in multiple cellular processes and linked with the pathogenesis of severa...

journal_title：Journal of chemical information and modeling

authors： Ombrato R,Cazzolla N,Mancini F,Mangano G

更新日期：2015-12-28 00:00:00

abstract：:We describe a novel deep learning neural network method and its application to impute assay pIC50 values. Unlike conventional machine learning approaches, this method is trained on sparse bioactivity data as input, typical of that found in public and commercial databases, enabling it to learn directly from correlation...

journal_title：Journal of chemical information and modeling

authors： Whitehead TM,Irwin BWJ,Hunt P,Segall MD,Conduit GJ

更新日期：2019-03-25 00:00:00

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

authors： Breu B,Silber K,Gohlke H

更新日期：2007-11-01 00:00:00

abstract：:A novel pharmacophore descriptor Flexophore is presented, which considers molecular flexibility when comparing descriptor similarities. The descriptor is a complete reduced graph of the underlying molecule. Its nodes are represented by enhanced MM2 atom types, while the edge descriptions encode the molecular flexibili...

journal_title：Journal of chemical information and modeling

authors： von Korff M,Freyss J,Sander T

更新日期：2008-04-01 00:00:00

abstract：:Deep learning methods applied to problems in chemoinformatics often require the use of recursive neural networks to handle data with graphical structure and variable size. We present a useful classification of recursive neural network approaches into two classes, the inner and outer approach. The inner approach uses r...

journal_title：Journal of chemical information and modeling

authors： Urban G,Subrahmanya N,Baldi P

更新日期：2018-02-26 00:00:00

abstract：:Three-dimensional protein structures are a key requisite for structure-based drug discovery. For many highly relevant targets, medicinal chemists are confronted with large numbers of target structures in their apo-forms or in complex with a wealth of different ligands. To exploit the full potential of such structure e...

journal_title：Journal of chemical information and modeling

authors： Schmalhorst PS,Bergner A

更新日期：2020-04-27 00:00:00

abstract：:SMIfp (SMILES fingerprint) is defined here as a scalar fingerprint describing organic molecules by counting the occurrences of 34 different symbols in their SMILES strings, which creates a 34-dimensional chemical space. Ligand-based virtual screening using the city-block distance CBD(SMIfp) as similarity measure provi...

journal_title：Journal of chemical information and modeling

authors： Schwartz J,Awale M,Reymond JL

更新日期：2013-08-26 00:00:00

abstract：:The integration of ligand- and structure-based strategies might sensitively increase the success of drug discovery process. We have recently described the application of Molecular Electrostatic Potential autocorrelated vectors (autoMEPs) in generating both linear (Partial Least-Square, PLS) and nonlinear (Response Sur...

journal_title：Journal of chemical information and modeling

authors： Michielan L,Bacilieri M,Schiesaro A,Bolcato C,Pastorin G,Spalluto G,Cacciari B,Klotz KN,Kaseda C,Moro S

更新日期：2008-02-01 00:00:00

abstract：:Herein we present the VMD Store, an open-source VMD plugin that simplifies the way that users browse, discover, install, update, and uninstall extensions for the Visual Molecular Dynamics (VMD) software. The VMD Store obtains data about all the indexed VMD extensions hosted on GitHub and presents a one-click mechanism...

journal_title：Journal of chemical information and modeling

authors： Fernandes HS,Sousa SF,Cerqueira NMFSA

更新日期：2019-11-25 00:00:00

abstract：:A novel approach was developed to rationally interface structure- and ligand-based drug design through the rescoring of docking poses and automated generation of molecular alignments for 3D quantitative structure-activity relationship investigations. The procedure was driven by a genetic algorithm optimizing the value...

journal_title：Journal of chemical information and modeling

authors： Nicolotti O,Miscioscia TF,Carotti A,Leonetti F,Carotti A

更新日期：2008-06-01 00:00:00

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 previo...

journal_title：Journal of chemical information and modeling

authors： Guha R,Jurs PC

更新日期：2005-01-01 00:00:00

abstract：:Flavonoids, the vastest class of natural polyphenols, are extensively investigated for their multiple benefits on human health. Due to their physicochemical or biological properties, many representatives are considered to exhibit low selectivity among various protein targets or to plague high-throughput screening (HTS...

journal_title：Journal of chemical information and modeling

authors： Avram SI,Pacureanu LM,Bora A,Crisan L,Avram S,Kurunczi L

更新日期：2014-08-25 00:00:00

abstract：:Protein-protein interactions are central to many biological processes, from intracellular communication to cytoskeleton assembly, and therefore represent an important class of targets for new therapeutics. The most common secondary structure in natural proteins is an α-helix. Small molecules seem to be attractive cand...

journal_title：Journal of chemical information and modeling

authors： Santos JS,Voisin-Chiret AS,Burzicki G,Sebaoun L,Sebban M,Lohier JF,Legay R,Oulyadi H,Bureau R,Rault S

更新日期：2012-02-27 00:00:00

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

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

abstract：:The binding affinity and relative maximal efficacy of human A3 adenosine receptor (AR) agonists were each subjected to ligand-based three-dimensional quantitative structure-activity relationship analysis. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) used a...

journal_title：Journal of chemical information and modeling

authors： Kimand SK,Jacobson KA

更新日期：2007-05-01 00:00:00

abstract：:Binding hot spots are regions of proteins that, due to their potentially high contribution to the binding free energy, have high propensity to bind small molecules. We present benchmark sets for testing computational methods for the identification of binding hot spots with emphasis on fragment-based ligand discovery. ...

journal_title：Journal of chemical information and modeling

authors： Wakefield AE,Yueh C,Beglov D,Castilho MS,Kozakov D,Keserű GM,Whitty A,Vajda S

更新日期：2020-12-28 00:00:00

abstract：:Great attention has been paid to the clinical significance of phosphodiesterase 5 (PDE5) inhibitors, such as sildenafil, tadalafil, and vardenafil widely used for erectile dysfunction. However, sildenafil causes side effects on visual functions since it shows similar potencies to inhibit PDE5 and PDE6, whereas tadalaf...

journal_title：Journal of chemical information and modeling

authors： Huang YY,Li Z,Cai YH,Feng LJ,Wu Y,Li X,Luo HB

更新日期：2013-11-25 00:00:00

abstract：:An essential feature of all practical de novo molecule generating programs is the ability to focus the potential combinatorial explosion of grown molecules on a desired chemical space. It is a daunting task to balance the generation of new molecules with limitations on growth that produce desired features such as stab...

journal_title：Journal of chemical information and modeling

authors： Kutchukian PS,Lou D,Shakhnovich EI

更新日期：2009-07-01 00:00:00

abstract：:Congeners are molecules based on the same carbon skeleton but are different by the number of substituents and/or a substitution pattern. Examples are 1-chloronaphthalene, 1,4-dichloronaphthalene, and 1,3,8-trichloronaphthalene. Various persistent organic pollutants (POPs) exist in the environment as families of congen...

journal_title：Journal of chemical information and modeling

authors： Haranczyk M,Urbaszek P,Ng EG,Puzyn T

更新日期：2012-11-26 00:00:00

abstract：:This study has assessed the use of consensus regression, as compared to single multiple linear regression, models for the development of quantitative structure-activity relationships (QSARs). To provide a comparison, four data sets of varying size and complexity were analyzed: silastic membrane flux, toxicity of pheno...

journal_title：Journal of chemical information and modeling

authors： Hewitt M,Cronin MT,Madden JC,Rowe PH,Johnson C,Obi A,Enoch SJ

更新日期：2007-07-01 00:00:00

abstract：:A homology model of the Arabidopsis thaliana UV resistance locus 8 (UVR8) protein is presented herein, showing a seven-bladed β-propeller conformation similar to the globular structure of RCC1. The UVR8 amino acid sequence contains a very high amount of conserved tryptophans, and the homology model shows that seven of...

journal_title：Journal of chemical information and modeling

authors： Wu M,Grahn E,Eriksson LA,Strid A

更新日期：2011-06-27 00:00:00

abstract：:A theoretical study of a variety of cyclohexane-based anion transporters interacting with the chloride anion has been conducted using density functional theory. The calculations have been performed in the gas phase but also, in order to describe the solvation effects on the interaction, two different solvents-chlorofo...

journal_title：Journal of chemical information and modeling

authors： Sánchez-Sanz G,Trujillo C

更新日期：2019-05-28 00:00:00

abstract：:An index of the activation of Class A G-protein-coupled receptors (GPCRs) has been trained using interhelix distances from a series of microsecond molecular-dynamics simulations and tested for 268 published X-ray structures. In a three-class model that includes intermediate structures, 63% of the active structures are...

journal_title：Journal of chemical information and modeling

authors： Ibrahim P,Wifling D,Clark T

更新日期：2019-09-23 00:00:00

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

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

更新日期：2020-10-26 00:00:00

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

authors： Zhu YL,Beroza P,Artis DR

更新日期：2014-02-24 00:00:00

abstract：:We report a novel method called ADAN (Applicability Domain ANalysis) for assessing the reliability of drug property predictions obtained by in silico methods. The assessment provided by ADAN is based on the comparison of the query compound with the training set, using six diverse similarity criteria. For every criteri...

journal_title：Journal of chemical information and modeling

authors： Carrió P,Pinto M,Ecker G,Sanz F,Pastor M

更新日期：2014-05-27 00:00:00

abstract：:Growing data sets with increased time for analysis is hampering predictive modeling in drug discovery. Model building can be carried out on high-performance computer clusters, but these can be expensive to purchase and maintain. We have evaluated ligand-based modeling on cloud computing resources where computations ar...

journal_title：Journal of chemical information and modeling

authors： Moghadam BT,Alvarsson J,Holm M,Eklund M,Carlsson L,Spjuth O

更新日期：2015-01-26 00:00:00

abstract：:Pharmacophore patterns in ligands can be effectively characterized in terms of their constituent pharmacophore multiplets. Bitsets (fingerprints) encoding which particular multiplets are found in a given ligand have been and continue to be used as molecular descriptors in a range of molecular modeling applications, fr...

journal_title：Journal of chemical information and modeling

authors： Fox PC,Wolohan PR,Abrahamian E,Clark RD

更新日期：2008-12-01 00:00:00

abstract：:This work is aimed at describing the workflow for a methodology that combines chemoinformatics and pharmacoepidemiology methods and at reporting the first predictive model developed with this methodology. The new model is able to predict complex networks of AIDS prevalence in the US counties, taking into consideration...

journal_title：Journal of chemical information and modeling

authors： González-Díaz H,Herrera-Ibatá DM,Duardo-Sánchez A,Munteanu CR,Orbegozo-Medina RA,Pazos A

更新日期：2014-03-24 00:00:00

abstract：:A compound's synthetic accessibility (SA) is an important aspect of drug design, since in some cases computer-designed compounds cannot be synthesized. There have been several reports on SA prediction, most of which have focused on the difficulties of synthetic reactions based on retro-synthesis analyses, reaction dat...

journal_title：Journal of chemical information and modeling

authors： Fukunishi Y,Kurosawa T,Mikami Y,Nakamura H

更新日期：2014-12-22 00:00:00