Use of surface charges from DFT calculations to predict intestinal absorption.

abstract：:When both the difference between two quantities and their individual values can be measured or computationally predicted, multiple quantities can be determined from the measurements or predictions of select individual quantities and select pairwise differences. These measurements and predictions form a network connect...

journal_title：Journal of chemical information and modeling

authors： Xu H

更新日期：2019-11-25 00:00:00

abstract：:HIV-1 replication requires binding to occur between Trans-activation Response Element (TAR) RNA and the TAT protein. This TAR-TAT binding depends on the conformation of TAR, and therapeutic development has attempted to exploit this dynamic behavior. Here we simulate TAR dynamics in the context of mutations inhibiting ...

journal_title：Journal of chemical information and modeling

authors： Krawczyk K,Sim AY,Knapp B,Deane CM,Minary P

更新日期：2016-09-26 00:00:00

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

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

更新日期：2009-08-01 00:00:00

abstract：:Traditional herbal medicine has been an inseparable part of the traditional medical science in many countries throughout history. Nowadays, the popularity of using herbal medicines in daily life, as well as clinical practices, has gradually expanded to numerous Western countries with positive impacts and acceptance. T...

journal_title：Journal of chemical information and modeling

authors： Nguyen-Vo TH,Nguyen L,Do N,Nguyen TN,Trinh K,Cao H,Le L

更新日期：2020-03-23 00:00:00

abstract：:A phenotypic screen (PS) is used to identify compounds causing a desired phenotype in a complex biological system where mechanisms and targets are largely unknown. Deconvoluting the mechanism of action of actives and identification of relevant targets and pathways remains a formidable challenge. Current methods fail t...

journal_title：Journal of chemical information and modeling

authors： Polyakov VR,Moorcroft ND,Drawid A

更新日期：2014-02-24 00:00:00

abstract：:Here, a method is described for easily building three-carbon nanotube junctions. It allows the geometry to be found and bond connectivity of C(3) symmetric nanotube junctions to be established. Such junctions may present a variable degree of pyramidalization and are composed of three identical carbon nanotubes with ar...

journal_title：Journal of chemical information and modeling

authors： Melchor S,Martin-Martinez FJ,Dobado JA

更新日期：2011-06-27 00:00:00

abstract：:The failure of default scoring functions to ensure virtual screening enrichment is a persistent problem for the molecular docking algorithms used in structure-based drug discovery. To remedy this problem, elaborate rescoring and postprocessing schemes have been developed with a varying degree of success, specificity, ...

journal_title：Journal of chemical information and modeling

authors： Kurkinen ST,Lätti S,Pentikäinen OT,Postila PA

更新日期：2019-08-26 00:00:00

abstract：:3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is a primary target in the current clinical treatment of hypercholesterolemia with specific inhibitors of "statin" family. Statins are excellent inhibitors of the class I (human) enzyme but relatively poor inhibitors of the class II enzyme, which are well-known as...

journal_title：Journal of chemical information and modeling

authors： Li D,Gui J,Li Y,Feng L,Han X,Sun Y,Sun T,Chen Z,Cao Y,Zhang Y,Zhou L,Hu X,Ren Y,Wan J

更新日期：2012-07-23 00:00:00

abstract：:The high-throughput docking protocol called ALTA-VS (anchor-based library tailoring approach for virtual screening) was developed in 2005 for the efficient in silico screening of large libraries of compounds by preselection of only those molecules that have optimal fragments (anchors) for the protein target. Here we p...

journal_title：Journal of chemical information and modeling

authors： Marchand JR,Dalle Vedove A,Lolli G,Caflisch A

更新日期：2017-10-23 00:00:00

abstract：:In this account, a rapid retrosynthesis-based scoring method for the assessment of synthetic accessibility of drug-like molecules, called RASA (Retrosynthesis-based Assessment of Synthetic Accessibility) is devised. RASA first constructs a synthesis tree for the target molecule based on retrosynthetic analysis; in thi...

journal_title：Journal of chemical information and modeling

authors： Huang Q,Li LL,Yang SY

更新日期：2011-10-24 00:00:00

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

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

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：:Due to the importance of hot-spots (HS) detection and the efficiency of computational methodologies, several HS detecting approaches have been developed. The current paper presents new models to predict HS for protein-protein and protein-nucleic acid interactions with better statistics compared with the ones currently...

journal_title：Journal of chemical information and modeling

authors： Munteanu CR,Pimenta AC,Fernandez-Lozano C,Melo A,Cordeiro MN,Moreira IS

更新日期：2015-05-26 00:00:00

abstract：:Herein we investigate whether QM/MM could prove useful as a tool to study the often subtle binding phenomena found within pharmaceutical drug discovery programs. The goal of this investigation is to determine whether it is possible to employ high level QM/MM calculations to answer specific questions around a binding e...

journal_title：Journal of chemical information and modeling

authors： Gleeson MP,Gleeson D

更新日期：2009-03-01 00:00:00

abstract：:Solubility parameter models are widely used to select suitable solvents/nonsolvents for polymers in a variety of processing and engineering applications. In this study, we focus on two well-established models, namely, the Hildebrand and Hansen solubility parameter models. Both models are built on the basis of the noti...

journal_title：Journal of chemical information and modeling

authors： Venkatram S,Kim C,Chandrasekaran A,Ramprasad R

更新日期：2019-10-28 00:00:00

abstract：:The antiproliferative factor (APF) involved in interstitial cystitis is a glycosylated nonapeptide (TVPAAVVVA) containing a sialylated core 1 α-O-disaccharide linked to the N-terminal threonine. The chemical structure of APF was deduced using spectroscopic techniques and confirmed using total synthesis. The synthetic ...

journal_title：Journal of chemical information and modeling

authors： Mallajosyula SS,Adams KM,Barchi JJ,MacKerell AD

更新日期：2013-05-24 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：: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：: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：:The industrial production of higher-generation semisynthetic cephalosporins starts from 7-aminocephalosporanic acid (7-ACA), which is obtained by deacylation of the naturally occurring antibiotic cephalosporin C (CephC). The enzymatic process in which CephC is directly converted into 7-ACA by a cephalosporin C acylase...

journal_title：Journal of chemical information and modeling

authors： Mollica L,Conti G,Pollegioni L,Cavalli A,Rosini E

更新日期：2015-10-26 00:00:00

abstract：:In this study we investigate π-stacking interactions of a variety of aromatic heterocycles with benzene using dispersion corrected density functional theory. We calculate extensive potential energy surfaces for parallel-displaced interaction geometries. We find that dispersion contributes significantly to the interact...

journal_title：Journal of chemical information and modeling

authors： Huber RG,Margreiter MA,Fuchs JE,von Grafenstein S,Tautermann CS,Liedl KR,Fox T

更新日期：2014-05-27 00:00:00

abstract：:Reactive oxygen species such as superoxide are potentially harmful byproducts of the aerobic metabolism in the inner mitochondrial membrane, and complexes I, II, III of the electron transport chain have been identified as primary sources. The mitochondrial fatty acid b-oxidation pathway may also play a yet uncharacter...

journal_title：Journal of chemical information and modeling

authors： Husen P,Nielsen C,Martino CF,Solov'yov IA

更新日期：2019-11-25 00:00:00

abstract：:Nonfibrillar neurotoxic amyloid β (Aβ) oligomer structures are typically rich in β-sheets, which could be promoted by metal ions like Zn(2+). Here, using molecular dynamics (MD) simulations, we systematically examined combinations of Aβ40 peptide conformations and Zn(2+) binding modes to probe the effects of secondary...

journal_title：Journal of chemical information and modeling

authors： Xu L,Shan S,Chen Y,Wang X,Nussinov R,Ma B

更新日期：2015-06-22 00:00:00

abstract：:The partitioning of amino acids between water and apolar environments is of vital importance in protein function and drug delivery. Here we present an extensive benchmark for octanol/water (log Poct), chloroform/water (log Pclf), and cyclohexane/water (log Pchx) partition coefficients of neutral amino acid side chain ...

journal_title：Journal of chemical information and modeling

authors： Zhang H,Jiang Y,Cui Z,Yin C

更新日期：2018-08-27 00:00:00

abstract：:Nonalcoholic hepatic steatosis is a worldwide epidemiological concern since it is among the most prominent hepatic diseases. Indeed, research in toxicology and epidemiology has gathered evidence that exposure to endocrine disruptors can perturb cellular homeostasis and cause this disease. Therefore, assessing the like...

journal_title：Journal of chemical information and modeling

authors： Gadaleta D,Manganelli S,Roncaglioni A,Toma C,Benfenati E,Mombelli E

更新日期：2018-08-27 00:00:00

abstract：:Ionotropic glutamate receptors (iGluRs) are synaptic proteins that facilitate signal transmission in the central nervous system. Extracellular iGluR cleft closure is linked to receptor activation; however, the mechanism underlying partial agonism is not entirely understood. Full agonists close the bilobed ligand-bindi...

journal_title：Journal of chemical information and modeling

authors： Postila PA,Ylilauri M,Pentikäinen OT

更新日期：2011-05-23 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：:Standardization is used to ensure that the variables in a similarity calculation make an equal contribution to the computed similarity value. This paper compares the use of seven different methods that have been suggested previously for the standardization of integer-valued or real-valued data, comparing the results w...

journal_title：Journal of chemical information and modeling

authors： Chu CW,Holliday JD,Willett P

更新日期：2009-02-01 00:00:00

abstract：:An important issue in developing protein-ligand docking methods is how to incorporate receptor flexibility. Consideration of receptor flexibility using an ensemble of precompiled receptor conformations or by employing an effectively enlarged binding pocket has been reported to be useful. However, direct consideration ...

journal_title：Journal of chemical information and modeling

authors： Shin WH,Seok C

更新日期：2012-12-21 00:00:00

abstract：:Homology modeling is a reliable method of predicting the three-dimensional structures of proteins that lack NMR or X-ray crystallographic data. It employs the assumption that a structural resemblance exists between closely related proteins. Despite the availability of many crystal structures of possible templates, onl...

journal_title：Journal of chemical information and modeling

authors： Rataj K,Witek J,Mordalski S,Kosciolek T,Bojarski AJ

更新日期：2014-06-23 00:00:00