Determination of Structural Ensembles of Flexible Molecules in Solution from NMR Data Undergoing Spin Diffusion.

abstract：:The Torsion Library contains hundreds of rules for small molecule conformations which have been derived from the Cambridge Structural Database (CSD) and are curated by molecular design experts. The torsion rules are encoded as SMARTS patterns and categorize rotatable bonds via a traffic light coloring scheme. We have ...

journal_title：Journal of chemical information and modeling

authors： Guba W,Meyder A,Rarey M,Hert J

更新日期：2016-01-25 00:00:00

abstract：:New hits against HIV-1 wild-type and Y181C drug-resistant reverse transcriptases were predicted taking into account the possibility of some of the known metabolism interactions. In silico hits against a set of antitargets (i.e., proteins or nucleic acids that are off-targets from the desired pharmaceutical target obje...

journal_title：Journal of chemical information and modeling

authors： García-Sosa AT,Sild S,Takkis K,Maran U

更新日期：2011-10-24 00:00:00

abstract：:We develop the idea that the use of ad hoc molecular descriptors in QSAR/QSPR studies is not an optimal solution. Instead, we propose to optimize these descriptors for the specific properties under study. In the case of topological indices (TIs) we propose the use of the generalized topological indices (GTIs), which a...

journal_title：Journal of chemical information and modeling

authors： Estrada E,Matamala AR

更新日期：2007-05-01 00:00:00

abstract：:We report the development of homology models of dopamine (D(2), D(3), and D(4)), serotonin (5-HT(1B), 5-HT(2A), 5-HT(2B), and 5-HT(2C)), histamine (H(1)), and muscarinic (M(1)) receptors, based on the high-resolution structure of the beta(2)-adrenergic receptor. The homology models were built and refined using Prime. ...

journal_title：Journal of chemical information and modeling

authors： McRobb FM,Capuano B,Crosby IT,Chalmers DK,Yuriev E

更新日期：2010-04-26 00:00:00

abstract：:Several hypotheses to elucidate the linkage isomer preference of the thiocyanate (SCN(-)) ion have been offered. For complexes with small coordination numbers (i.e., 1 and 2) and groups 11 (Cu-triad) and 12 (Zn-triad) metals, different levels of theory and a variety of basis sets have been employed to study linkage is...

journal_title：Journal of chemical information and modeling

authors： Buda C,Kazi AB,Dinescu A,Cundari TR

更新日期：2005-07-01 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：:Throughout the drug discovery process, discovery teams are compelled to use statistics for making decisions using data from a variety of inputs. For instance, teams are asked to prioritize compounds for subsequent stages of the drug discovery process, given results from multiple screens. To assist in the prioritizatio...

journal_title：Journal of chemical information and modeling

authors： Mandal A,Johnson K,Wu CF,Bornemeier D

更新日期：2007-05-01 00:00:00

abstract：:Dual and triple activity-difference (DAD/TAD) maps are tools for the systematic characterization of structure-activity relationships (SAR) of compound data sets screened against two or three targets. DAD and TAD maps are two- and three- dimensional representations of the pairwise activity differences of compound data ...

journal_title：Journal of chemical information and modeling

authors： Medina-Franco JL,Yongye AB,Pérez-Villanueva J,Houghten RA,Martínez-Mayorga K

更新日期：2011-09-26 00:00:00

abstract：:Saturated acyclic alkanes show steric strain if they are highly branched and, in extreme cases, fall apart rapidly at room temperature. Consequently, attempts to count the number of isomeric forms for a given molecular formula that neglect this physical consideration will inevitably overestimate the size of the availa...

journal_title：Journal of chemical information and modeling

authors： Paton RS,Goodman JM

更新日期：2007-11-01 00:00:00

abstract：:Structure-based virtual screening relies on classical scoring functions that often fail to reliably discriminate binders from nonbinders. In this work, we present a high-throughput protein-ligand complex molecular dynamics (MD) simulation that uses the output from AutoDock Vina to improve docking results in distinguis...

journal_title：Journal of chemical information and modeling

authors： Guterres H,Im W

更新日期：2020-04-27 00:00:00

abstract：:Searching chemical databases for possible drug leads is often one of the main activities conducted during the early stages of a drug development project. This article shows that spherical harmonic molecular shape representations provide a powerful way to search and cluster small-molecule databases rapidly and accurate...

journal_title：Journal of chemical information and modeling

authors： Mavridis L,Hudson BD,Ritchie DW

更新日期：2007-09-01 00:00:00

abstract：:Due to the recent availability of high quality small molecule databases, such as ZINC and PubChem,1,2 virtual screening is playing an even more important role in identifying biologically relevant molecules in drug discovery campaigns. The success of pharmacophore-based virtual screening (PBVS) relies largely on the ac...

journal_title：Journal of chemical information and modeling

authors： Jia L,Zou J,So SS,Sun H

更新日期：2007-07-01 00:00:00

abstract：:Central to Hsp90's biological function is its ability to interconvert between various conformational states. Drug targeting of Hsp90's regulatory mechanisms, including its modulation by cochaperone association, presents as an attractive therapeutic strategy for Hsp90 associated pathologies. In this study, we utilized ...

journal_title：Journal of chemical information and modeling

authors： Penkler DL,Atilgan C,Tastan Bishop Ö

更新日期：2018-02-26 00:00:00

abstract：:New molecular descriptors, RED (Renyi entropy descriptors), based on the generalized entropies introduced by Renyi are presented. Topological descriptors based on molecular features have proven to be useful for describing molecular profiles. Renyi entropy is used as a variability measure to contract a feature-pair dis...

journal_title：Journal of chemical information and modeling

authors： Delgado-Soler L,Toral R,Tomás MS,Rubio-Martinez J

更新日期：2009-11-01 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：:Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishin...

journal_title：Journal of chemical information and modeling

authors： Zhang Q,Xu Z,Shi J,Zhu W

更新日期：2017-07-24 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：:We propose an improved solvent contact model to estimate the solvation free energy of an organic molecule from individual atomic contributions. The modification of the solvation model involves the optimization of three kinds of parameters in the solvation free energy function: atomic fragmental volume, maximum atomic ...

journal_title：Journal of chemical information and modeling

authors： Kang H,Choi H,Park H

更新日期：2007-03-01 00:00:00

abstract：:In this work, we report an ab initio investigation based on density functional theory calculations within van der Waals D3 corrections to investigate the adsorption properties and activation of CO2 on transition-metal (TM) 13-atom clusters (TM = Ru, Rh, Pd, Ag), which is a key step for the development of subnano catal...

journal_title：Journal of chemical information and modeling

authors： Batista KEA,Ocampo-Restrepo VK,Soares MD,Quiles MG,Piotrowski MJ,Da Silva JLF

更新日期：2020-02-24 00:00:00

abstract：:The predictive performances of MC4PC were evaluated using its learning machine functionality. Its superior characteristics are demonstrated in this following up study using the newly published Ames mutagenicity benchmark set. ...

journal_title：Journal of chemical information and modeling

authors： Saiakhov RD,Klopman G

更新日期：2010-09-27 00:00:00

abstract：:SIRT2, which is a NAD+ (nicotinamide adenine dinucleotide) dependent deacetylase, has been demonstrated to play an important role in the occurrence and development of a variety of diseases such as cancer, ischemia-reperfusion, and neurodegenerative diseases. Small molecule inhibitors of SIRT2 are thought to be potenti...

journal_title：Journal of chemical information and modeling

authors： Huang S,Song C,Wang X,Zhang G,Wang Y,Jiang X,Sun Q,Huang L,Xiang R,Hu Y,Li L,Yang S

更新日期：2017-04-24 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：:The efficiency of automated compound screening is heavily influenced by the design and the quality of the screening libraries used. We recently reported on the assembly of one diverse and one target-focused lead-like screening library. Using data from 15 enzyme-based screenings conducted using these libraries, their p...

journal_title：Journal of chemical information and modeling

authors： Mok NY,Maxe S,Brenk R

更新日期：2013-03-25 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：:We propose a hypothesis that "a model of active compound can be provided by integrating information of compounds high-ranked by docking simulation of a random compound library". In our hypothesis, the inclusion of true active compounds in the high-ranked compound is not necessary. We regard the high-ranked compounds a...

journal_title：Journal of chemical information and modeling

authors： Fukunishi H,Teramoto R,Shimada J

更新日期：2008-03-01 00:00:00

abstract：:A kinetic, reactivity-binding model has been proposed to predict the regioselectivity of substrates meditated by the CYP1A2 enzyme, which is responsible for the metabolism of planar-conjugated compounds such as caffeine. This model consists of a docking simulation for binding energy and a semiempirical molecular orbit...

journal_title：Journal of chemical information and modeling

authors： Jung J,Kim ND,Kim SY,Choi I,Cho KH,Oh WS,Kim DN,No KT

更新日期：2008-05-01 00:00:00

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：:We used synthetic peloruside A for the commercial preparation of [³H]peloruside A. The radiolabeled compound bound to preformed tubulin polymer in amounts stoichiometric with the polymer's tubulin content, with an apparent K(d) value of 0.35 μM. A less active peloruside A analogue, (11-R)-peloruside A and laulimalide ...

journal_title：Journal of chemical information and modeling

authors： Nguyen TL,Xu X,Gussio R,Ghosh AK,Hamel E

更新日期：2010-11-22 00:00:00

abstract：:A database has been derived from recently reported [60]fullerene derivatives, and their binding scores with HIV-1 PR have been computed using docking techniques. Computational methods have been used to predict which derivatives may have high binding affinities, and for these compounds biological tests have been perfor...

journal_title：Journal of chemical information and modeling

authors： Durdagi S,Supuran CT,Strom TA,Doostdar N,Kumar MK,Barron AR,Mavromoustakos T,Papadopoulos MG

更新日期：2009-05-01 00:00:00

abstract：:We investigate unexpectedly short non-covalent distances (<85% of the sum of van der Waals radii) in X-ray crystal structures of proteins. We curate over 11 000 high-quality protein crystal structures and an ultra-high-resolution (1.2 Å or better) subset containing >900 structures. Although our non-covalent distance c...

journal_title：Journal of chemical information and modeling

authors： Qi HW,Kulik HJ

更新日期：2019-05-28 00:00:00