Prediction of pH-dependent aqueous solubility of druglike molecules.

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：:On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, a...

journal_title：Journal of chemical information and modeling

authors： Clark AM,Dole K,Coulon-Spektor A,McNutt A,Grass G,Freundlich JS,Reynolds RC,Ekins S

更新日期：2015-06-22 00:00:00

abstract：:A compound's synthetic accessibility (SA) is an important aspect of drug design, since in some cases computer-designed compounds cannot be synthesized. There have been several reports on SA prediction, most of which have focused on the difficulties of synthetic reactions based on retro-synthesis analyses, reaction dat...

journal_title：Journal of chemical information and modeling

authors： Fukunishi Y,Kurosawa T,Mikami Y,Nakamura H

更新日期：2014-12-22 00:00:00

abstract：:Classical nonpolarizable models, normally based on a combination of Lennard-Jones sites and point charges, are extensively used to model thermodynamic properties of fluids, including solvation. An important shortcoming of these models is that they do not explicitly account for polarization effects, i.e., a description...

journal_title：Journal of chemical information and modeling

authors： Barrera MC,Jorge M

更新日期：2020-03-23 00:00:00

abstract：:We propose predictive performance criteria for nonlinear regression models without cross-validation. The proposed criteria are the determination coefficient and the root-mean-square error for the midpoints between k-nearest-neighbor data points. These criteria can be used to evaluate predictive ability after the regre...

journal_title：Journal of chemical information and modeling

authors： Kaneko H,Funatsu K

更新日期：2013-09-23 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：:We introduce the statistics behind a novel type of SAR analysis named "nonadditivity analysis". On the basis of all pairs of matched pairs within a given data set, the approach analyzes whether the same transformations between related molecules have the same effect, i.e., whether they are additive. Assuming that the e...

journal_title：Journal of chemical information and modeling

authors： Kramer C

更新日期：2019-09-23 00:00:00

abstract：:A major concern of chemogenomics is to associate drug activity with biological variables. Several reports have clustered cell line drug activity profiles as well as drug activity-gene expression correlation profiles and noted that the resulting groupings differ but still reflect mechanism of action. The present paper ...

journal_title：Journal of chemical information and modeling

authors： Andersson CR,Fryknäs M,Rickardson L,Larsson R,Isaksson A,Gustafsson MG

更新日期：2007-01-01 00:00:00

abstract：:Template CoMFA, a novel alignment methodology for training or test set structures in 3D-QSAR, is introduced. Its two most significant advantages are its complete automation and its ability to derive a single combined model from multiple structural series affecting a biological target. Its only two inputs are one or mo...

journal_title：Journal of chemical information and modeling

authors： Cramer RD,Wendt B

更新日期：2014-02-24 00:00:00

abstract：:Pharmacophore hypotheses were developed for six structurally diverse series of cholecystokinin-B/gastrin receptor (CCK-BR) antagonists. A training set consisting of 33 compounds was carefully selected. The activity spread of the training set molecules was from 0.1 to 2100 nM. The most predictive pharmacophore model (h...

journal_title：Journal of chemical information and modeling

authors： Chopra M,Mishra AK

更新日期：2005-11-01 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：: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：:We present an algorithm, ReFlex3D, for the refinement of flexible molecular alignments based on their three-dimensional shape and electrostatic properties. The algorithm is designed to be used with fast conformer generators to refine an initial overlay between two molecules and thus to obtain improved overlaps as judg...

journal_title：Journal of chemical information and modeling

authors： Schmidt TC,Cosgrove DA,Boström J

更新日期：2018-04-23 00:00:00

abstract：:A new methodology to describe the interactions in "receptor-ligand" complexes is presented. The methodology is based on a combination of the 3D/4D QSAR BiS/MC and CoCon algorithms. The first algorithm performs the restricted docking of compounds to receptor pockets. The second determines the relationships between the ...

journal_title：Journal of chemical information and modeling

authors： Potemkin VA,Pogrebnoy AA,Grishina MA

更新日期：2009-06-01 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：:Generalization of an earlier algorithm has led to the development of new local structural alignment algorithms for prediction of protein-protein binding sites. The algorithms use maximum cliques on protein graphs to define structurally similar protein regions. The search for structural neighbors in the new algorithms ...

journal_title：Journal of chemical information and modeling

authors： Carl N,Konc J,Vehar B,Janezic D

更新日期：2010-10-25 00:00:00

abstract：:The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In th...

journal_title：Journal of chemical information and modeling

authors： Won J,Lee GR,Park H,Seok C

更新日期：2018-06-25 00:00:00

abstract：:Grass weed populations resistant to acetyl-CoA carboxylase-inhibiting (ACCase; EC 6.4.1.2) herbicides represent a major problem for the sustainable development of modern agriculture. In the present study, extensive computational simulations, including homology modeling, molecular dynamics (MD) simulations, and molecul...

journal_title：Journal of chemical information and modeling

authors： Zhu XL,Ge-Fei H,Zhan CG,Yang GF

更新日期：2009-08-01 00:00:00

abstract：:Moving to a new country, with a different culture and a new environment, is not an easy decision. In this perspective, I present some reasons that made me, a Brazilian computational biochemist, move abroad to do postdoctoral research and some of the challenges I faced before and after moving. ...

journal_title：Journal of chemical information and modeling

authors： Nunes-Alves A

更新日期：2020-02-24 00:00:00

abstract：:Molecular fragment dynamics (MFD) is a variant of dissipative particle dynamics (DPD), a coarse-grained mesoscopic simulation technique for isothermal complex fuids and soft matter systems with particles that are chosen to be adequate fluid elements. MFD choses its particles to be small molecules which may be connecte...

journal_title：Journal of chemical information and modeling

authors： Truszkowski A,van den Broek K,Kuhn H,Zielesny A,Epple M

更新日期：2015-05-26 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：:Sixteen FDA-approved drugs were investigated to elucidate their mechanisms of action (MOAs) and clinical functions by pathway analysis based on retrieved drug targets interacting with or affected by the investigated drugs. Protein and gene targets and associated pathways were obtained by data-mining of public database...

journal_title：Journal of chemical information and modeling

authors： Pan Y,Cheng T,Wang Y,Bryant SH

更新日期：2014-02-24 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：:The human cytochrome P450 1A2 is an important drug metabolizing and procarcinogen activating enzyme. An experimental study found that a peripheral mutation, F186L, at ∼26 Å away from the enzyme's active site, caused a significant reduction in the enzymatic activity of 1A2 deethylation reactions. In this paper, we expl...

journal_title：Journal of chemical information and modeling

authors： Zhang T,Liu LA,Lewis DF,Wei DQ

更新日期：2011-06-27 00:00:00

abstract：:The sensitivity of docking calculations to the geometry of the input ligand was studied. It was found that even small changes in the ligand input conformation can lead to large differences in the geometries and scores of the resulting docked poses. The accuracy of docked poses produced from different ligand input stru...

journal_title：Journal of chemical information and modeling

authors： Feher M,Williams CI

更新日期：2009-07-01 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：:The homodimeric catabolite activator protein (CAP) regulates the transcription of several bacterial genes based on the cellular concentration of cyclic adenosine monophosphate (cAMP). The binding of cAMP to CAP triggers allosteric communication between the cAMP binding domains (CBD) and DNA binding domains (DBD) of CA...

journal_title：Journal of chemical information and modeling

authors： Prabhakant A,Panigrahi A,Krishnan M

更新日期：2020-12-28 00:00:00

abstract：:G protein-coupled receptors (GPCRs) represent the largest family of cell-surface receptors and about one-third of the actual targets of clinically used drugs. Following the progress made in the field of GPCRs structural determination, docking-based screening for novel potent and selective ligands is becoming an increa...

journal_title：Journal of chemical information and modeling

authors： Sabbadin D,Ciancetta A,Moro S

更新日期：2014-01-27 00:00:00

abstract：:In this work, the perception of similarity of reactions catalyzed by hydrolases and oxidoreductases on the basis of the overall breaking and making of bonds of reactions is investigated. Six physicochemical properties for the reacting bond in the substrate of each enzymatic reaction were calculated to describe the cha...

journal_title：Journal of chemical information and modeling

authors： Hu X,Yan A,Tan T,Sacher O,Gasteiger J

更新日期：2010-06-28 00:00:00

abstract：:Increased reports of oseltamivir (OTV)-resistant strains of the influenza virus, such as the H274Y mutation on its neuraminidase (NA), have created some cause for concern. Many studies have been conducted in the attempt to uncover the mechanism of OTV resistance in H274Y NA. However, most of the reported studies on H2...

journal_title：Journal of chemical information and modeling

authors： Yusuf M,Mohamed N,Mohamad S,Janezic D,Damodaran KV,Wahab HA

更新日期：2016-01-25 00:00:00