Multitarget structure-activity relationships characterized by activity-difference maps and consensus similarity measure.

abstract：:Proteins often have both orthosteric and allosteric binding sites. Endogenous ligands, such as hormones and neurotransmitters, bind to the orthosteric site, while synthetic ligands may bind to orthosteric or allosteric sites, which has become a focal point in drug discovery. Usually, such allosteric modulators bind to...

journal_title：Journal of chemical information and modeling

authors： Burggraaff L,van Veen A,Lam CC,van Vlijmen HWT,IJzerman AP,van Westen GJP

更新日期：2020-10-26 00:00:00

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

authors： Pottel J,Moitessier N

更新日期：2017-03-27 00:00:00

abstract：:The COSMO surface polarization charge density σ resulting from quantum chemical calculations combined with a virtual conductor embedding has been widely proven to be a very suitable descriptor for the quantification of interactions of molecules in liquids. In a preceding paper, grid-based local histograms of σ have be...

journal_title：Journal of chemical information and modeling

authors： Klamt A,Thormann M,Wichmann K,Tosco P

更新日期：2012-08-27 00:00:00

abstract：:Advances in the development of high-throughput screening and automated chemistry have rapidly accelerated the production of chemical and biological data, much of them freely accessible through literature aggregator services such as ChEMBL and PubChem. Here, we explore how to use this comprehensive mapping of chemical ...

journal_title：Journal of chemical information and modeling

authors： Zakharov AV,Zhao T,Nguyen DT,Peryea T,Sheils T,Yasgar A,Huang R,Southall N,Simeonov A

更新日期：2019-11-25 00:00:00

abstract：:Protein-polysaccharide complexes constructed via self-assembly methods are often used to develop novel biomaterials for a wide range of applications in biomedicine, food, and biotechnology. The objective of this work was to investigate theoretically and to demonstrate via constant-pH Monte Carlo simulations that the c...

journal_title：Journal of chemical information and modeling

authors： Prudkin-Silva C,Pérez OE,Martínez KD,Barroso da Silva FL

更新日期：2020-02-24 00:00:00

abstract：:Metal-ligand (M-L) bond lengths for a range of ligands (carboxylates, chlorides, pyridines, water, tertiary phosphines, and alkenes) and a variety of metals have been retrieved from the Cambridge Structural Database, CSD. Analysis of the factors which affect M-L bond lengths (for example, ligand coordination mode, oxi...

journal_title：Journal of chemical information and modeling

authors： Harris SE,Orpen AG,Bruno IJ,Taylor R

更新日期：2005-11-01 00:00:00

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

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

更新日期：2012-12-21 00:00:00

abstract：:Compounds with high-confidence target annotations and activity measurements in the original and current release of the ChEMBL database have been compared to better understand how the growth of compound activity data might influence the spectrum of ligand-target interactions and the degree of target promiscuity among a...

journal_title：Journal of chemical information and modeling

authors： Hu Y,Bajorath J

更新日期：2012-10-22 00:00:00

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

authors： Namasivayam V,Bajorath J

更新日期：2012-04-23 00:00:00

abstract：:Following the theoretical model by Hann et al. moderately complex structures are preferable lead compounds since they lead to specific binding events involving the complete ligand molecule. To make this concept usable in practice for library design, we studied several complexity measures on the biological activity of ...

journal_title：Journal of chemical information and modeling

authors： Schuffenhauer A,Brown N,Selzer P,Ertl P,Jacoby E

更新日期：2006-03-01 00:00:00

abstract：:Understanding the relationship between chemical structure and function is a ubiquitous problem within the fields of chemistry and biology. Simulation approaches attack the problem utilizing physics to understand a given process at the particle level. Unfortunately, these approaches are often too expensive for many pro...

journal_title：Journal of chemical information and modeling

authors： Brown WM,Sasson A,Bellew DR,Hunsaker LA,Martin S,Leitao A,Deck LM,Vander Jagt DL,Oprea TI

更新日期：2008-08-01 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：:Theoretical calculation of equilibrium dissociation constants is a very computationally demanding and time-consuming process since it requires an extremely accurate computation of the solvation free energy changes for each of the species involved. By correlating the minimum surface electrostatic potential (VS,min) on ...

journal_title：Journal of chemical information and modeling

authors： Sandoval-Lira J,Mondragón-Solórzano G,Lugo-Fuentes LI,Barroso-Flores J

更新日期：2020-03-23 00:00:00

abstract：:To promote more productive combinatorial endeavors, the Diversity Space methodology introduced here enables similarity comparisons at the library level. Particularly at an early screening stage, when little or no information is available regarding the pharmacophoric entities necessary for binding, it is more efficient...

journal_title：Journal of chemical information and modeling

authors： Fitzgerald SH,Sabat M,Geysen HM

更新日期：2006-07-01 00:00:00

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

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

abstract：:Solute-solvent interactions are critical for biomolecular stability and recognition. Explicit solvent molecular dynamics (MD) simulations are routinely used to probe such interactions. However, detailed analyses and interpretation of the hydration patterns seen in MD simulations can be both complex and time-consuming....

journal_title：Journal of chemical information and modeling

authors： Pradhan MR,Nguyen MN,Kannan S,Fox SJ,Kwoh CK,Lane DP,Verma CS

更新日期：2019-07-22 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：:The interaction between small molecules and proteins is one of the major concerns for structure-based drug design because the principles of protein-ligand interactions and molecular recognition are not thoroughly understood. Fortunately, the analysis of protein-ligand complexes in the Protein Data Bank (PDB) enables u...

journal_title：Journal of chemical information and modeling

authors： Wang L,Xie Z,Wipf P,Xie XQ

更新日期：2011-04-25 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：: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：: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

authors： Da C,Kireev D

更新日期：2014-09-22 00:00:00

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

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

更新日期：2005-11-01 00:00:00

abstract：:Most drugs exert their effects via multitarget interactions, as hypothesized by polypharmacology. While these multitarget interactions are responsible for the clinical effect profiles of drugs, current methods have failed to uncover the complex relationships between them. Here, we introduce an approach which is able t...

journal_title：Journal of chemical information and modeling

authors： Simon Z,Peragovics A,Vigh-Smeller M,Csukly G,Tombor L,Yang Z,Zahoránszky-Kohalmi G,Végner L,Jelinek B,Hári P,Hetényi C,Bitter I,Czobor P,Málnási-Csizmadia A

更新日期：2012-01-23 00:00:00

abstract：:Novel statistical potentials derived from known protein structures are presented. They are designed to describe cation-pi and amino-pi interactions between a positively charged amino acid or an amino acid carrying a partially charged amino group and an aromatic moiety. These potentials are based on the propensity of r...

journal_title：Journal of chemical information and modeling

authors： Gilis D,Biot C,Buisine E,Dehouck Y,Rooman M

更新日期：2006-03-01 00:00:00

abstract：:The in silico prediction of unwanted side effects (SEs) caused by the promiscuous behavior of drugs and their targets is highly relevant to the pharmaceutical industry. Considerable effort is now being put into computational and experimental screening of several suspected off-target proteins in the hope that SEs might...

journal_title：Journal of chemical information and modeling

authors： Pérez-Nueno VI,Souchet M,Karaboga AS,Ritchie DW

更新日期：2015-09-28 00:00:00

abstract：:The more that is known about human and other genome sequences and the correlation between gene expression and the course of a disease, the more evident it seems to be that DNA is chosen as a drug target instead of proteins which are built with the information encoded by DNA. According to this approach, small minor gro...

journal_title：Journal of chemical information and modeling

authors： Spitzer GM,Wellenzohn B,Laggner C,Langer T,Liedl KR

更新日期：2007-07-01 00:00:00

abstract：:Alanine scanning is a tool in molecular biology that is commonly used to evaluate the contribution of a specific amino acid residue to the stability and function of a protein. Additionally, this tool is also used to understand whether the side chain of a specific amino acid residue plays a role in the protein's bioact...

journal_title：Journal of chemical information and modeling

authors： Coskuner-Weber O,Uversky VN

更新日期：2019-02-25 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：:All molecules of up to 11 atoms of C, N, O, and F possible under consideration of simple valency, chemical stability, and synthetic feasibility rules were generated and collected in a database (GDB). GDB contains 26.4 million molecules (110.9 million stereoisomers), including three- and four-membered rings and triple ...

journal_title：Journal of chemical information and modeling

authors： Fink T,Reymond JL

更新日期：2007-03-01 00:00:00

abstract：:Atomic neural networks (ANNs) constitute a class of machine learning methods for predicting potential energy surfaces and physicochemical properties of molecules and materials. Despite many successes, developing interpretable ANN architectures and implementing existing ones efficiently are still challenging. This call...

journal_title：Journal of chemical information and modeling

authors： Shao Y,Hellström M,Mitev PD,Knijff L,Zhang C

更新日期：2020-03-23 00:00:00