SMIfp (SMILES fingerprint) chemical space for virtual screening and visualization of large databases of organic molecules.

abstract：:The chronic toxicity is fundamental for toxicological risk assessment, but its correlation with the chemical structures has been studied only little. This is partly due to the complexity of such an experimental test that embraces a plethora of different biological effects and mechanisms of action, making (Q)SAR studie...

journal_title：Journal of chemical information and modeling

authors： Mazzatorta P,Estevez MD,Coulet M,Schilter B

更新日期：2008-10-01 00:00:00

abstract：:With the hope of discovering effective analgesics with fewer side effects, attention has recently shifted to allosteric modulators of the opioid receptors. In the past two years, the first chemotypes of positive or silent allosteric modulators (PAMs or SAMs, respectively) of μ- and δ-opioid receptor types have been re...

journal_title：Journal of chemical information and modeling

authors： Bisignano P,Burford NT,Shang Y,Marlow B,Livingston KE,Fenton AM,Rockwell K,Budenholzer L,Traynor JR,Gerritz SW,Alt A,Filizola M

更新日期：2015-09-28 00:00:00

abstract：:In a departure from conventional chemical approaches, data-driven models of chemical reactions have recently been shown to be statistically successful using machine learning. These models, however, are largely black box in character and have not provided the kind of chemical insights that historically advanced the fie...

journal_title：Journal of chemical information and modeling

authors： Kammeraad JA,Goetz J,Walker EA,Tewari A,Zimmerman PM

更新日期：2020-03-23 00:00:00

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

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

更新日期：2011-01-24 00:00:00

abstract：:A new radial space-filling method for visualizing cluster hierarchies is presented. The method, referred to as a radial clustergram, arranges the clusters into a series of layers, each representing a different level of the tree. It uses adjacency of nodes instead of links to represent parent-child relationships and al...

journal_title：Journal of chemical information and modeling

authors： Agrafiotis DK,Bandyopadhyay D,Farnum M

更新日期：2007-01-01 00:00:00

abstract：:Small molecule flexible alignment is a critical component of both ligand- and structure-based methods in computer-aided drug discovery. Despite its importance, the availability of high-quality flexible alignment software packages is limited. Here, we present BCL::MolAlign, a freely available property-based molecular a...

journal_title：Journal of chemical information and modeling

authors： Brown BP,Mendenhall J,Meiler J

更新日期：2019-02-25 00:00:00

abstract：:Protein-protein interactions (PPIs) play vital roles in regulating biological processes, such as cellular and signaling pathways. Hotspots are certain residues located at protein-protein interfaces that contribute more in protein-protein binding than other residues. Research on the mutational effects of hotspots is im...

journal_title：Journal of chemical information and modeling

authors： Wu FX,Yang JF,Mei LC,Wang F,Hao GF,Yang GF

更新日期：2021-01-25 00:00:00

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

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

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：: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：:A new structure classification scheme for biopolymers is introduced, which is solely based on main-chain dihedral angles. It is shown that by dividing a biopolymer into segments containing two central residues, a local classification can be performed. The method is referred to as DISICL, short for Dihedral-based Segme...

journal_title：Journal of chemical information and modeling

authors： Nagy G,Oostenbrink C

更新日期：2014-01-27 00:00:00

abstract：:Model lipid membranes made from binary mixtures of dimyristoylphosphatidylcholine/dipalmitoylphosphatidylcholine (DMPC/DPPC) and dimyristoylphosphatidylcholine/cholesterol (DMPC/Chol) exhibit coexistence of diverse lipid phases at appropriate temperature and composition. Since lipids in different phases show different...

journal_title：Journal of chemical information and modeling

authors： Arsov Z,Strancar J

更新日期：2005-11-01 00:00:00

abstract：:Fast and accurate predicting of the binding affinities of large sets of diverse protein−ligand complexes is an important, yet extremely challenging, task in drug discovery. The development of knowledge-based scoring functions exploiting structural information of known protein−ligand complexes represents a valuable con...

journal_title：Journal of chemical information and modeling

authors： Shen Q,Xiong B,Zheng M,Luo X,Luo C,Liu X,Du Y,Li J,Zhu W,Shen J,Jiang H

更新日期：2011-02-28 00:00:00

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

authors： Ivanciuc T,Ivanciuc O,Klein DJ

更新日期：2005-07-01 00:00:00

abstract：:We report here on long-time all-atomistic molecular dynamics simulations of functional supramolecular nanotubes composed by the self-assembly of peptide-drug amphiphiles (DAs). These DAs have been shown to possess an inherently high drug loading of the hydrophobic anticancer drug camptothecin. We probe the self-assemb...

journal_title：Journal of chemical information and modeling

authors： Kang M,Chakraborty K,Loverde SM

更新日期：2018-06-25 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：: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

authors： Amangeldiuly N,Karlov D,Fedorov MV

更新日期：2020-12-28 00:00:00

abstract：:Distribution patterns of 8411 compounds from 240 Chinese herbs were analyzed in relation to the herbal categories of traditional Chinese medicine (TCM), using Random Forest (RF) and self-organizing maps (SOM). RF was used first to construct TCM profiles of individual compounds, which describe their affinities for 28 m...

journal_title：Journal of chemical information and modeling

authors： Ehrman TM,Barlow DJ,Hylands PJ

更新日期：2007-11-01 00:00:00

abstract：:We introduce SARANEA, an open-source Java application for interactive exploration of structure-activity relationship (SAR) and structure-selectivity relationship (SSR) information in compound sets of any source. SARANEA integrates various SAR and SSR analysis functions and utilizes a network-like similarity graph data...

journal_title：Journal of chemical information and modeling

authors： Lounkine E,Wawer M,Wassermann AM,Bajorath J

更新日期：2010-01-01 00:00:00

abstract：:While critically reviewing the current status of what is known about C28H14 and C30H14 benzenoid isomers, which are ubiquitous pyrolytic constituents, some new insights will be presented. Representative isomers belonging to these benzenoid hydrocarbons are at the crossroads to homologous series that extend to infinite...

journal_title：Journal of chemical information and modeling

authors： Dias JR

更新日期：2006-03-01 00:00:00

abstract：:A MMGBSA variant (here referred to as Nwat-MMGBSA), based on the inclusion of a certain number of explicit water molecules (Nwat) during the calculations, has been tested on a set of 20 protein-protein complexes, using the correlation between predicted and experimental binding energy as the evaluation metric. Besides ...

journal_title：Journal of chemical information and modeling

authors： Maffucci I,Contini A

更新日期：2016-09-26 00:00:00

abstract：:Estrogens exert important physiological effects through the modulation of two human estrogen receptor (hER) subtypes, alpha (hERalpha) and beta (hERbeta). Because the levels and relative proportion of hERalpha and hERbeta differ significantly in different target cells, selective hER ligands could target specific tissu...

journal_title：Journal of chemical information and modeling

authors： Salum LB,Polikarpov I,Andricopulo AD

更新日期：2008-11-01 00:00:00

abstract：:In this DFT study, activities of 11 different N2O4, N2O3, and NO2 core containing Zr(IV) complexes, 4,13-diaza-18-crown-6 (I'N2O4), 1,4,10-trioxa-7,13-diazacyclopentadecane (I'N2O3), and 2-(2-methoxy)ethanol (I'NO2), respectively, and their analogues in peptide hydrolysis have been investigated. Based on the experimen...

journal_title：Journal of chemical information and modeling

authors： Zhang T,Sharma G,Paul TJ,Hoffmann Z,Prabhakar R

更新日期：2017-05-22 00:00:00

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

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

更新日期：2019-02-25 00:00:00

abstract：:We have applied the two most commonly used methods for automatic matched pair identification, obtained the optimum settings, and discovered that the two methods are synergistic. A turbocharging approach to matched pair analysis is advocated in which a first round (a conservative categorical approach that uses an analo...

journal_title：Journal of chemical information and modeling

authors： Lukac I,Zarnecka J,Griffen EJ,Dossetter AG,St-Gallay SA,Enoch SJ,Madden JC,Leach AG

更新日期：2017-10-23 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：:There is a renewed interest in computer-aided synthesis planning, where the vast majority of approaches require the application of retrosynthetic reaction templates. Here we introduce RDChiral, an open-source Python wrapper for RDKit designed to provide consistent handling of stereochemical information in applying ret...

journal_title：Journal of chemical information and modeling

authors： Coley CW,Green WH,Jensen KF

更新日期：2019-06-24 00:00:00

abstract：:A machine learning enhanced spectrum recognition system called spectrum recognition based on computer vision (SRCV) for data extraction from previously analyzed 13C and 1H NMR spectra has been developed. The intelligent system was designed with four function modules to extract data from three areas of NMR images, incl...

journal_title：Journal of chemical information and modeling

authors： Jia W,Yang Z,Yang M,Cheng L,Lei Z,Wang X

更新日期：2021-01-25 00:00:00

abstract：:Determination of structural similarities between protein binding pockets is an important challenge in in silico drug design. It can help to understand selectivity considerations, predict unexpected ligand cross-reactivity, and support the putative annotation of function to orphan proteins. To this end, Cavbase was dev...

journal_title：Journal of chemical information and modeling

authors： Krotzky T,Grunwald C,Egerland U,Klebe G

更新日期：2015-01-26 00:00:00

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

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

更新日期：2006-11-01 00:00:00