Abstract:
:An online resource has been developed for the theoretical study of hydration of biopolymers by the RISM (Reference Interaction Site Model) method, deriving from the integral equation theory of liquids. The online resource is based upon original software developed by the authors and includes all steps in studying a biopolymer with a given spatial structure and force field. It prepares the input data and carries out the RISM calculation yielding the atom-atom correlation functions of the biopolymer with water as solvent. From these functions the algorithm finds atomic partial contributions to the hydration free energy using various free energy expressions from integral equation theory. The calculated results are automatically recorded in a database, and become available on the website as tables of partial thermodynamic quantities. In addition, the website displays an interactive 3D model of a given molecule, the atoms of which can be painted in different colors in accordance with their partial contributions to the thermodynamic quantity chosen by the user. The user can interactively choose atoms on this molecule and their correlation functions will be displayed. The aim of our work was to develop and present a publicly-accessible resource on the basis of original software which could be used for scientific and educational purposes.
journal_name
SAR QSAR Environ Resjournal_title
SAR and QSAR in environmental researchauthors
Sobolev EV,Sobolev OV,Tikhonov DAdoi
10.1080/10629360802083707subject
Has Abstractpub_date
2008-04-01 00:00:00pages
303-15issue
3-4eissn
1062-936Xissn
1029-046Xpii
793155543journal_volume
19pub_type
杂志文章abstract::As often noted by Dr. Gilman Veith, a major barrier to advancing any model is defining its applicability domain. Sulfur-containing industrial organic chemicals can be grouped into several chemical classes including mercaptans (RSH), sulfides (RSR'), disulfides (RSSR'), sulfoxides (RS(=O)R'), sulfones (RS(=O)(=O)R'), s...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2014.898693
更新日期:2014-01-01 00:00:00
abstract::It is well known that bromodomain-containing protein 4 (BRD4) has been thought as a promising target utilized for treating various human diseases, such as inflammatory disorders, malignant tumours, acute myelogenous leukaemia (AML), bone diseases, etc. For this study, molecular dynamics (MD) simulations, binding free ...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2020.1777584
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abstract::On the basis of computer prediction of biological activity by PASS and toxicity by DEREK, the most prospective 18 alkylaminoacyl derivatives of 3-amino-benzo-[d]-isothiazole were selected. Their local anesthetic action was assessed using an in vitro preparation of the isolated peroneal nerve of the frog. The local ane...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/10629360310001624051
更新日期:2003-10-01 00:00:00
abstract::This paper presents the application of the MTD (minimal steric difference) analysis and CoMFA (comparative molecular field analysis) to series of anthraquinone vat, mono and disazo and disperses dyes with known affinities for cellulose fiber. A comparison of the results demonstrates that these methods usually agree wi...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/10629360290002703
更新日期:2002-03-01 00:00:00
abstract::The limited availability and variability of data related to atmospheric degradation reaction is a very relevant issue in studies related to environmental fate and behavior of chemicals. For screening purposes, the experimental data of the oxidation rate constants for the reactions with the radicals OH, NO3 and with oz...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936021000043472
更新日期:2002-12-01 00:00:00
abstract::Chagas disease is endemic to 21 Latin American countries and is a great public health problem in that region. Current chemotherapy remains unsatisfactory; consequently the need to search for new drugs persists. Here we present a new approach to identify novel compounds with potential anti-chagasic action. A large data...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2020.1863857
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abstract::Artificial neural networks (ANN) can be used for the direct QSAR analysis of percent effect biological data, thus avoiding the bias introduced by arbitrarily chosen classes and the loss of information due to prior classification. For two data sets the ANN results are compared with those obtained by adaptive least squa...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/10629369308028825
更新日期:1993-01-01 00:00:00
abstract::An improved binary differential search (improved BDS) algorithm is proposed for QSAR classification of diverse series of antimicrobial compounds against Candida albicans inhibitors. The transfer functions is the most important component of the BDS algorithm, and converts continuous values of the donor into discrete va...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2019.1568298
更新日期:2019-02-01 00:00:00
abstract::Gas phase acidity and basicity estimation models have been developed for acidic and basic functional groups of amino acid side-chains and also for a number of small organic molecules. The acidic functional groups include aliphatic and aromatic alcohol, and aliphatic and aromatic carboxylic acid, and the basic function...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2013.864997
更新日期:2014-01-01 00:00:00
abstract::Pair-correlation method (PCM) has been developed for selecting between two, correlated descriptor variables. PCM utilizes systematic information present in the scatter of QSAR applications. The data are suitably ordered in a 2 x 2 contingency table. Statistical tests are used to discriminate between the descriptor var...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/10629360290023368
更新日期:2002-07-01 00:00:00
abstract::Existing toxicological data may be used for a variety of purposes such as hazard and risk assessment or toxicity prediction. The potential use of such data is, in part, dependent upon their quality. Consideration of data quality is of key importance with respect to the application of chemicals legislation such as REAC...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2012.664825
更新日期:2012-07-01 00:00:00
abstract::The base-line modeling concept presented in this work is based on the assumption of a maximum bioconcentration factor (BCF) with mitigating factors that reduce the BCF. The maximum bioconcentration potential was described by the multi-compartment partitioning model for passive diffusion. The significance of different ...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/10659360500474623
更新日期:2005-12-01 00:00:00
abstract::The Quantitative Ion Character-Activity Relationship (QICAR) method was used for correlating metal ionic characteristics with the maximum adsorption capacity (qmax) of multi-walled carbon for heavy metals. The experimental values of qmax for 25 heavy metal ions, estimated by the Langmuir isotherm model, were used to c...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2018.1538059
更新日期:2018-12-01 00:00:00
abstract::In this work, a descriptor, SVRG (principal component scores vector of radial distribution function descriptors and geometrical descriptors), was derived from principal component analysis (PCA) of a matrix of two structural variables of coded amino acids, including radial distribution function index (RDF) and geometri...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2011.604099
更新日期:2011-07-01 00:00:00
abstract::The development of more efficient, ethical, and effective means of assessing the effects of chemicals on human health and the environment was a lifetime goal of Gilman Veith. His work has provided the foundation for the use of chemical structure for informing toxicological assessment by regulatory agencies the world o...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2014.907203
更新日期:2014-01-01 00:00:00
abstract::The current study deals with chemometric modelling strategies (Naïve Bayes classification, hologram-based quantitative structure-activity relationship (HQSAR), comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA)) to explore the important features of hydroxylamine d...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2018.1447511
更新日期:2018-05-01 00:00:00
abstract::COX-2 inhibitors exhibit anticancer effects in various cancer models but due to the adverse side effects associated with these inhibitors, targeting molecules downstream of COX-2 (such as mPGES-1) has been suggested. Even after calls for mPGES-1 inhibitor design, to date there are only a few published inhibitors targe...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2016.1273971
更新日期:2017-01-01 00:00:00
abstract::This article represents a minireview of work published so far in the 21st century in the in silico ADMET field of research related to investigations in the areas of solubility, hERG and cytochrome P450 3A4. Various approaches including 2D- and 3D-QSARs and pharmacophore modelling are discussed. The pros and cons of th...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章,评审
doi:10.1080/10629360412331319835
更新日期:2005-02-01 00:00:00
abstract::With the ever-growing number of xenobiotics that can potentially contaminate the environment, the determination of their mammalian toxicity is of prime importance. In this context, LD50 tests on rats and mice have been used for a long time to express the relative hazard associated with the acute toxicity of inorganic ...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章,评审
doi:10.1080/10629360903278651
更新日期:2009-07-01 00:00:00
abstract::A series of our SAR and QSAR studies of synthetic moulting hormone agonists, dibenzoylhydrazines (DBH), exhibiting insecticidal/larvicidal activity are reviewed in this article. We prepared a number of analogues where various substituents are introduced into the two benzene rings of DBH and measured their biological a...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章,评审
doi:10.1080/10629360601053943
更新日期:2007-01-01 00:00:00
abstract::Genotoxicity is a key toxicity endpoint for current regulatory requirements regarding new and existing chemicals. However, genotoxicity testing is time-consuming and costly, and involves the use of laboratory animals. This has motivated the development of computational approaches, designed to predict genotoxicity with...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2013.820791
更新日期:2014-01-01 00:00:00
abstract::The electrotopological state (E-State) and its extension, the atom-type E-State, is presented as a representation of atom and molecular fragment structure useful for chemical database organization and management. An approach to database organization, using substituted esters and benzene derivatives as examples, reveal...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/10629360108035371
更新日期:2001-01-01 00:00:00
abstract::Knowledge of the interpolative region or applicability domain (AD) of structure-activity relationships is believed to improve predictive accuracy. The present work was undertaken to characterize the AD of EPI Suite biotransformation models and evaluate the performance of selected AD assessment methods. AD methods were...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2010.501816
更新日期:2010-07-01 00:00:00
abstract::Traditional knowledge guides the use of plants for restricted therapeutic indications, but their pharmacological actions may be found beyond their ethnic therapeutic indications employing emerging computational tools. In this context, the present study was envisaged to explore the novel pharmacological effect of Achyr...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2017.1408683
更新日期:2018-01-01 00:00:00
abstract::The evaluation of persistency of chemicals in environmental media (water, soil, sediment) is included in European Regulations, in the context of the Persistence, Bioaccumulation and Toxicity (PBT) assessment. In silico predictions are valuable alternatives for compounds screening and prioritization. However, already e...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2020.1776387
更新日期:2020-07-01 00:00:00
abstract::Three modelling systems (MultiCase®, LeadScope® and MDL® QSAR) were used for construction of androgenic receptor antagonist models. There were 923-942 chemicals in the training sets. The models were cross-validated (leave-groups-out) with concordances of 77-81%, specificity of 78-91% and sensitivity of 51-76%. The spe...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2010.528981
更新日期:2011-03-01 00:00:00
abstract::Modern industrialisation has led to the production of millions of toxic chemicals having hazardous effects on the ecosystem. It is impracticable to determine the toxic potential of a large number of chemicals in animal models, making the use of quantitative structure-toxicity relationship (QSTR) models an alternative ...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2011.645872
更新日期:2012-01-01 00:00:00
abstract::CORAL software has been used to build quantitative structure-activity relationships (QSARs) for the prediction of binding affinities (pEC50, i.e., minus decimal logarithm of the 50% effective concentration) of 35 potent inhibitors towards the voltage-gated potassium channel subunit Kv7.2. The pEC50 has been modelled u...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2013.842930
更新日期:2014-01-01 00:00:00
abstract::Matrix metalloproteinase-2 (MMP-2) is a potential target in anticancer drug discovery due to its association with angiogenesis, metastasis and tumour progression. In this study, 67 glutamic acid derivatives, synthesized and evaluated as MMP-2 inhibitors, were taken into account for multi-QSAR modelling study (regressi...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/1062936X.2017.1406986
更新日期:2018-01-01 00:00:00
abstract::Over half of known industrial pollutants have minimal toxic effect, in line with the concept of "baseline toxicity"; such toxicity usually correlates well with lipophilicity. The remainder require additional descriptors in order to model their toxicity by the QSAR approach. Hence, it has not been possible, to date, to...
journal_title:SAR and QSAR in environmental research
pub_type: 杂志文章
doi:10.1080/10629360412331297498
更新日期:2004-10-01 00:00:00