Aggregation properties of a polymeric anticancer therapeutic: a coarse-grained modeling study.

abstract：:The modeling of nonlinear descriptor-target relationships is a topic of considerable interest in drug discovery. We, herein, continue reporting the use of the self-organizing map-a nonlinear, topology-preserving pattern recognition technique that exhibits considerable promise in modeling and decoding these relationshi...

journal_title：Journal of chemical information and modeling

authors： Xiao YD,Harris R,Bayram E,Ii PS,Schmitt JD

更新日期：2006-01-01 00:00:00

abstract：:The concept of chemoisosterism of protein environments is introduced as the complementary property to bioisosterism of chemical fragments. In the same way that two chemical fragments are considered bioisosteric if they can bind to the same protein environment, two protein environments will be considered chemoisosteric...

journal_title：Journal of chemical information and modeling

authors： Jalencas X,Mestres J

更新日期：2013-02-25 00:00:00

abstract：:The human androgen receptor (AR) is a ligand-activated transcription factor that plays a pivotal role in the development and progression of prostate cancer (PCa). Many forms of castration-resistant prostate cancer (CRPC) still rely on the AR for survival. Currently used antiandrogens face clinical limitations as drug ...

journal_title：Journal of chemical information and modeling

authors： Paul N,Carabet LA,Lallous N,Yamazaki T,Gleave ME,Rennie PS,Cherkasov A

更新日期：2016-12-27 00:00:00

abstract：:A giant technological leap in the field of cryo-electron microscopy (cryo-EM) has assured the achievement of near-atomic resolution structures of biological macromolecules. As a recognition of this accomplishment, the Nobel Prize in Chemistry was awarded in 2017 to Jacques Dubochet, Joachim Frank, and Richard Henderso...

journal_title：Journal of chemical information and modeling

authors： Akbar S,Mozumder S,Sengupta J

更新日期：2020-05-26 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：:QSPR studies, using scores of SciTegic's extended connectivity fingerprint as raw descriptors, were extended to the prediction of melting points and aqueous solubility of organic compounds. Robust partial least-squares models were developed that perform as well as the best published QSPR models for structurally divers...

journal_title：Journal of chemical information and modeling

authors： Zhou D,Alelyunas Y,Liu R

更新日期：2008-05-01 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：: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

authors： Randić M,Balaban AT

更新日期：2006-01-01 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：:Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TRalpha and TRbeta. Several pharmacological effects mediated by TRbeta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TRbeta activation may el...

journal_title：Journal of chemical information and modeling

authors： Valadares NF,Salum LB,Polikarpov I,Andricopulo AD,Garratt RC

更新日期：2009-11-01 00:00:00

abstract：:The community structure-activity resource (CSAR) data sets are used to develop and test a support vector machine-based scoring function in regression mode (SVR). Two scoring functions (SVR-KB and SVR-EP) are derived with the objective of reproducing the trend of the experimental binding affinities provided within the ...

journal_title：Journal of chemical information and modeling

authors： Li L,Wang B,Meroueh SO

更新日期：2011-09-26 00:00:00

abstract：:We have studied the binding affinities of a set of 45 small-molecule inhibitors to protein tyrosine phosphatase 1B (PTP1B) through computational approaches. All of these compounds share a common oxalylamino benzoic acid (OBA) moiety. The complex structure of each compound was modeled by using the GOLD program plus the...

journal_title：Journal of chemical information and modeling

authors： Zhang X,Li X,Wang R

更新日期：2009-04-01 00:00:00

abstract：:Methods that rapidly evaluate molecular complexity and synthetic feasibility are becoming increasingly important for in silico chemistry. We propose a new metric based on relative atomic electronegativities and bond parameters that evaluate both synthetic and molecular complexity (SMCM) starting from chemical structur...

journal_title：Journal of chemical information and modeling

authors： Allu TK,Oprea TI

更新日期：2005-09-01 00:00:00

abstract：:Small molecules targeting peripheral CB1 receptors have therapeutic potential in a variety of disorders including obesity-related, hormonal, and metabolic abnormalities, while avoiding the psychoactive effects in the central nervous system. We applied our in-house algorithm, iterative stochastic elimination, to produc...

journal_title：Journal of chemical information and modeling

authors： El-Atawneh S,Hirsch S,Hadar R,Tam J,Goldblum A

更新日期：2019-09-23 00:00:00

abstract：:In this article, we present a systematic way to classify a family of high-genus fullerenes (HGFs) by decomposing them into two types of necklike structures, which are the negatively curved parts of parent toroidal carbon nanotubes. By replacing the faces of a uniform polyhedron with these necks, an HGF polyhedron corr...

journal_title：Journal of chemical information and modeling

authors： Chuang C,Jin BY

更新日期：2009-07-01 00:00:00

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

authors： Ruiz IL,Gómez-Nieto MÁ

更新日期：2017-11-27 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：:Various cages are constructed by using three types of caps: f-cap (derived from spherical fullerenes by deleting zones of various size), kf-cap (obtainable by cutting off the polar ring, of size k), and t-cap ("tubercule"-cap). Building ways are presented, some of them being possible isomerization routes in the real c...

journal_title：Journal of chemical information and modeling

authors： Diudea MV,Nagy CL,Silaghi-Dumitrescu I,Graovac A,Janezic D,Vikić-Topić D

更新日期：2005-03-01 00:00:00

abstract：:In this work, we present molecular modeling studies carried out using six DNA sequences and six azinomycin analogues, including the naturally occurring compound azinomycin B, selected on the basis of known cell cytotoxicity and structural analogies (epoxide and aziridine alkylating moieties). Among several computation...

journal_title：Journal of chemical information and modeling

authors： Alcaro S,Ortuso F,Coleman RS

更新日期：2005-05-01 00:00:00

abstract：:Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies tha...

journal_title：Journal of chemical information and modeling

authors： Moriya Y,Yamada T,Okuda S,Nakagawa Z,Kotera M,Tokimatsu T,Kanehisa M,Goto S

更新日期：2016-03-28 00:00:00

abstract：:Covalent inhibitors have been gaining increased attention in drug discovery due to their beneficial properties such as long residence time, high biochemical efficiency, and specificity. Optimization of covalent inhibitors is a complex task that involves parallel monitoring of the noncovalent recognition elements and t...

journal_title：Journal of chemical information and modeling

authors： Mihalovits LM,Ferenczy GG,Keserű GM

更新日期：2020-12-28 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：:Binding free energy calculations that make use of alchemical pathways are becoming increasingly feasible thanks to advances in hardware and algorithms. Although relative binding free energy (RBFE) calculations are starting to find widespread use, absolute binding free energy (ABFE) calculations are still being explore...

journal_title：Journal of chemical information and modeling

authors： Aldeghi M,Bodkin MJ,Knapp S,Biggin PC

更新日期：2017-09-25 00:00:00

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

authors： Zhang QY,Aires-de-Sousa J

更新日期：2006-11-01 00:00:00

abstract：:The metabolism of xenobiotics--and more specifically drugs--in the liver is a critical process controlling their half-life. Although there exist experimental methods, which measure the metabolic stability of xenobiotics and identify their metabolites, developing higher throughput predictive methods is an avenue of res...

journal_title：Journal of chemical information and modeling

authors： Campagna-Slater V,Pottel J,Therrien E,Cantin LD,Moitessier N

更新日期：2012-09-24 00:00:00

abstract：:In this study, we aimed to develop a new ligand-based virtual screening approach using an effective shape-overlapping procedure and a more robust scoring function (denoted by the HWZ score for convenience). The HWZ score-based virtual screening approach was tested against the compounds for 40 protein targets available...

journal_title：Journal of chemical information and modeling

authors： Hamza A,Wei NN,Zhan CG

更新日期：2012-04-23 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：:Ergotamine (ERG) and dihydroergotamine (DHE), common migraine drugs, have small structural differences but lead to clinically important distinctions in their pharmacological profiles. For example, DHE is less potent than ERG by about 10-fold at the 5-hydroxytrptamine receptor 1B (5-HT1B). Although the high-resolution ...

journal_title：Journal of chemical information and modeling

authors： Sullivan HJ,Tursi A,Moore K,Campbell A,Floyd C,Wu C

更新日期：2020-03-23 00:00:00

abstract：:Drug-induced torsade de pointes (TdP) is a life-threatening ventricular arrhythmia responsible for the withdrawal of many drugs from the market. Although currently used TdP risk-assessment methods are effective, they are expensive and prone to produce false positives. In recent years, in silico cardiac simulations hav...

journal_title：Journal of chemical information and modeling

authors： Llopis-Lorente J,Gomis-Tena J,Cano J,Romero L,Saiz J,Trenor B

更新日期：2020-10-26 00:00:00

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

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

更新日期：2013-02-25 00:00:00