Abstract:
:The dissolution of a chemical into water is a process fundamental to both chemistry and biology. The persistence of a chemical within the environment and the effects of a chemical within the body are dependent primarily upon aqueous solubility. With the well-documented limitations hindering the accurate experimental determination of aqueous solubility, the utilization of predictive methods have been widely investigated and employed. The setting of a solubility challenge by this journal proved an excellent opportunity to explore several different modeling methods, utilizing a supplied dataset of high-quality aqueous solubility measurements. Four contrasting approaches (simple linear regression, artificial neural networks, category formation, and available in silico models) were utilized within our laboratory and the quality of these predictions was assessed. These were chosen to span the multitude of modeling methods now in use, while also allowing for the evaluation of existing commercial solubility models. The conclusions of this study were surprising, in that a simple linear regression approach proved to be superior over more complex modeling methods. Possible explanations for this observation are discussed and also recommendations are made for future solubility prediction.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Hewitt M,Cronin MT,Enoch SJ,Madden JC,Roberts DW,Dearden JCdoi
10.1021/ci900286ssubject
Has Abstractpub_date
2009-11-01 00:00:00pages
2572-87issue
11eissn
1549-9596issn
1549-960Xjournal_volume
49pub_type
杂志文章abstract::Development of coarse-grained (CG) molecular dynamics models is often a laborious process which commonly relies upon approximations to similar models, rather than systematic parametrization. PyCGTOOL automates much of the construction of CG models via calculation of both equilibrium values and force constants of inter...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00096
更新日期:2017-04-24 00:00:00
abstract::Scoring the activity of compounds in phenotypic high-throughput assays presents a unique challenge because of the limited resolution and inherent measurement error of these assays. Techniques that leverage the structural similarity of compounds within an assay can be used to improve the hit-recovery rate from screenin...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci050087d
更新日期:2005-11-01 00:00:00
abstract::The purpose of this investigation is to contribute to the development of new anticonvulsant drugs to treat patients with refractory epilepsy. We applied a virtual screening protocol that involved the search into molecular databases of new compounds and known drugs to find small molecules that interact with the open co...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00721
更新日期:2018-07-23 00:00:00
abstract::A new structure classification scheme for biopolymers is introduced, which is solely based on main-chain dihedral angles. It is shown that by dividing a biopolymer into segments containing two central residues, a local classification can be performed. The method is referred to as DISICL, short for Dihedral-based Segme...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci400541d
更新日期:2014-01-27 00:00:00
abstract::Functional diversity of the three-finger-protein domain (TFPD) had been acquired via hypervariability of some sequence positions and extensive insertion/deletion of short AA-segments that caused multidimensional drift of several sequence attributes such as the overall (HI) and local hydrophobicity levels, the isoelect...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.5b00322
更新日期:2015-09-28 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
pub_type: 杂志文章
doi:10.1021/ci600235w
更新日期:2006-11-01 00:00:00
abstract::Distribution patterns of 8411 compounds from 240 Chinese herbs were analyzed in relation to the herbal categories of traditional Chinese medicine (TCM), using Random Forest (RF) and self-organizing maps (SOM). RF was used first to construct TCM profiles of individual compounds, which describe their affinities for 28 m...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci700155t
更新日期:2007-11-01 00:00:00
abstract::Dynamical properties of proteins play an essential role in their function exertion. The elastic network model (ENM) is an effective and efficient tool in characterizing the intrinsic dynamical properties encoded in biomacromolecule structures. The Gaussian network model (GNM) and anisotropic network model (ANM) are th...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.0c01178
更新日期:2021-01-26 00:00:00
abstract::An essential feature of all practical de novo molecule generating programs is the ability to focus the potential combinatorial explosion of grown molecules on a desired chemical space. It is a daunting task to balance the generation of new molecules with limitations on growth that produce desired features such as stab...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci9000458
更新日期:2009-07-01 00:00:00
abstract::The effects of paclitaxel (PTX) loading fraction and spatial PTX arrangement on poly(γ-glutamyl-glutamate) paclitaxel (PGG-PTX) aggregation were explored using coarse-grained molecular dynamics. Results show that the PTX loading fraction does not significantly impact aggregation, and the spatial PTX arrangement only a...
journal_title:Journal of chemical information and modeling
pub_type: 信件
doi:10.1021/ci200214m
更新日期:2011-12-27 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
pub_type: 杂志文章
doi:10.1021/ci500760m
更新日期:2015-05-26 00:00:00
abstract::Physicochemical properties of compounds have been instrumental in selecting lead compounds with increased drug-likeness. However, the relationship between physicochemical properties of constituent drugs and the tendency to exhibit drug interaction has not been systematically studied. We assembled physicochemical descr...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci500276x
更新日期:2014-08-25 00:00:00
abstract::Factor Xa inhibitors are innovative anticoagulant agents that provide a better safety/efficacy profile compared to other anticoagulative drugs. A chemical feature-based modeling approach was applied to identify crucial pharmacophore patterns from 3D crystal structures of inhibitors bound to human factor Xa (Pdb entrie...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci049778k
更新日期:2005-01-01 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
pub_type: 杂志文章
doi:10.1021/ci800419j
更新日期:2009-03-01 00:00:00
abstract::Membrane fusion, a key step in the early stages of virus propagation, allows the release of the viral genome in the host cell cytoplasm. The process is initiated by fusion peptides that are small, hydrophobic components of viral membrane-embedded glycoproteins and are typically conserved within virus families. Here, w...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.0c01231
更新日期:2021-01-25 00:00:00
abstract::Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to ...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.9b00665
更新日期:2019-10-28 00:00:00
abstract::Computer programs for structure diagram generation (SDG) are indispensable cheminformatic tools that translate one- or three-dimensional (1D or 3D) chemical structure data stored in electronic formats to human-readable 2D depictions. Although many such programs are known, only a moderate part of chemical space can be ...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.6b00391
更新日期:2016-12-27 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
pub_type: 杂志文章
doi:10.1021/ci400696v
更新日期:2014-02-24 00:00:00
abstract::The quantitative structure-activity relationship (QSAR) approach has been used to model a wide range of chemical-induced biological responses. However, it had not been utilized to model chemical-induced genomewide gene expression changes until very recently, owing to the complexity of training and evaluating a very la...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00281
更新日期:2017-09-25 00:00:00
abstract::A generic chemical transformation may often be achieved under various synthetic conditions. However, for any specific reagents, only one or a few among the reported synthetic protocols may be successful. For example, Michael β-addition reactions may proceed under different choices of solvent (e.g., hydrophobic, aproti...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci500698a
更新日期:2015-02-23 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
pub_type: 杂志文章
doi:10.1021/ci7001507
更新日期:2007-09-01 00:00:00
abstract::Among the photophysical parameters that underpin Förster resonance energy transfer (FRET), perhaps the least explored is the spectral overlap term ( J). While by definition J increases linearly with acceptor molar absorption coefficient (ε(A) in M-1 cm-1), is proportional to wavelength (λ4), and depends on the degree ...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.8b00753
更新日期:2019-02-25 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
pub_type: 杂志文章
doi:10.1021/acs.jcim.0c00201
更新日期:2020-10-26 00:00:00
abstract::The current drug virtual screen (VS) methods mainly include two categories. i.e., ligand/target structure-based virtual screen and that, utilizing protein-ligand interaction fingerprint information based on the large number of complex structures. Since the former one focuses on the one-side information while the later...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci200481c
更新日期:2012-03-26 00:00:00
abstract::The integration of ligand- and structure-based strategies might sensitively increase the success of drug discovery process. We have recently described the application of Molecular Electrostatic Potential autocorrelated vectors (autoMEPs) in generating both linear (Partial Least-Square, PLS) and nonlinear (Response Sur...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci700300w
更新日期:2008-02-01 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
pub_type: 杂志文章
doi:10.1021/ci3003304
更新日期:2012-10-22 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
pub_type: 评论,信件
doi:10.1021/ci1000899
更新日期:2010-09-27 00:00:00
abstract::The emergence of a large amount of pharmacological, genomic, and network knowledge data provides new challenges and opportunities for drug discovery and development. Identification of real small-molecule drug (SM)-miRNA associations is not only important in the development of effective drug repositioning but also cruc...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.0c00244
更新日期:2020-08-24 00:00:00
abstract::In this study, we have developed a two model system to mimic the active and inactive states of a G-protein coupled receptor specifically the alpha1A adrenergic receptor. We have docked two agonists, epinephrine (phenylamine type) and oxymetazoline (imidazoline type), as well as two antagonists, prazosin and 5-methylur...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci700026v
更新日期:2007-09-01 00:00:00
abstract::Molecular dynamics simulations provide valuable insights into the behavior of molecular systems. Extending the recent trend of using machine learning techniques to predict physicochemical properties from molecular dynamics data, we propose to consider the trajectories as multidimensional time series represented by 2D ...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.9b00135
更新日期:2019-08-26 00:00:00