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1.
SAR QSAR Environ Res ; 17(1): 1-10, 2006 Feb.
Article in English | MEDLINE | ID: mdl-16513548

ABSTRACT

Nowadays the in silico scenario for drug design is totally dependent on structural biology and structural bioinformatics. A myriad of free bioinformatics applications and services have been posted on the web. This mini-review mentions web sites that are useful in structure-based drug design. The information is given in a logical manner, following the drug design process i.e. characterization of a protein target, modelling the protein using sequence homology, optimization of the protein structure and finally docking of small ligands into the active site.


Subject(s)
Computational Biology , Drug Design , Proteins/chemistry , Amino Acid Sequence , Databases, Factual , Sequence Alignment
2.
SAR QSAR Environ Res ; 17(1): 93-105, 2006 Feb.
Article in English | MEDLINE | ID: mdl-16513554

ABSTRACT

A model for rainbow trout (Oncorhynchus mykiss) estrogen receptor (rtERa) was built by homology with the human estrogen receptor (hERa). A high level of sequence conservation between the two receptors was found with 64% and 80% of identity and similarity, respectively. Selected endocrine disrupting chemicals were docked into the ligand binding domain (LBD) of rtERa and the corresponding free binding energies Delta(DeltaG(bind)) values were calculated. A Quantitative Structure-Activity Relationship (QSAR) model between the relative binding affinity data and the Delta(DeltaG(bind)) values was derived in order to predict which further organic pollutants are likely to bind to rtERa.


Subject(s)
Endocrine System/drug effects , Estrogen Receptor alpha/chemistry , Models, Molecular , Amino Acid Sequence , Animals , Humans , Molecular Sequence Data , Oncorhynchus mykiss , Sequence Homology, Amino Acid
3.
SAR QSAR Environ Res ; 15(1): 43-54, 2004 Feb.
Article in English | MEDLINE | ID: mdl-15113068

ABSTRACT

Among computational chemistry methods, quantum mechanics calculates geometries and electronic structures with accuracy especially for systems with electronic delocalization. The use of a multiconfigurational approach is able to treat highly degenerated states such as those occurring at the transition state in some chemical reactions. Moreover, an accurate description of potential energy surfaces can be obtained with the evaluation of the dynamic electron correlation effects by this approach. Molecular properties range from simple dipole moments, vibrational frequencies or IR intensities to frequency dependent hyperpolarizabilities. Quantum chemical calculations are thus an attractive source of molecular descriptors which can be used in QSAR/QSPR studies and which can express all electronic and geometric properties of molecules. A survey and a comparison of the performance of free e-resources for semi-empirical and ab initio calculations is provided.


Subject(s)
Data Collection , Models, Chemical , Quantum Theory , Information Services , Molecular Conformation , Quantitative Structure-Activity Relationship
4.
SAR QSAR Environ Res ; 14(5-6): 329-37, 2003.
Article in English | MEDLINE | ID: mdl-14758977

ABSTRACT

Due to recent computer technology advances, shape analysis has gained importance in all domains. In drug design and proteomics, molecular surfaces (van der Waals surface, solvent accessible surface, solvent excluded surface, polar surface area, electron density surface, separating surface, etc.), buried surfaces (gap, cleft, cavity, etc.) as well as shape properties of these surfaces, can be easily computed and visualized via the Internet. Freely available resources from the Internet for academic use, are reviewed.


Subject(s)
Drug Design , Internet , Models, Molecular , Computer Simulation , Quantitative Structure-Activity Relationship , Software
5.
SAR QSAR Environ Res ; 13(3-4): 403-8, 2002.
Article in English | MEDLINE | ID: mdl-12184381

ABSTRACT

Computational chemistry and molecular modeling sites have proliferated on the Internet's world wide web. This paper provides present links to some of the more most useful ones for small organic molecule modeling, and offering free resources.


Subject(s)
Internet , Models, Chemical , Molecular Structure , Chemistry/trends , Organic Chemicals , Structure-Activity Relationship
6.
Food Chem Toxicol ; 40(2-3): 145-91, 2002.
Article in English | MEDLINE | ID: mdl-11893397

ABSTRACT

This paper is one of several prepared under the project "Food Safety In Europe: Risk Assessment of Chemicals in Food and Diet" (FOSIE), a European Commission Concerted Action Programme, organised by the International Life Sciences Institute, Europe (ILSI). The aim of the FOSIE project is to review the current state of the science of risk assessment of chemicals in food and diet, by consideration of the four stages of risk assessment, that is, hazard identification, hazard characterisation, exposure assessment and risk characterisation. The contribution of animal-based methods in toxicology to hazard identification of chemicals in food and diet is discussed. The importance of first applying existing technical and chemical knowledge to the design of safety testing programs for food chemicals is emphasised. There is consideration of the presently available and commonly used toxicity testing approaches and methodologies, including acute and repeated dose toxicity, reproductive and developmental toxicity, neurotoxicity, genotoxicity, carcinogenicity, immunotoxicity and food allergy. They are considered from the perspective of whether they are appropriate for assessing food chemicals and whether they are adequate to detect currently known or anticipated hazards from food. Gaps in knowledge and future research needs are identified; research on these could lead to improvements in the methods of hazard identification for food chemicals. The potential impact of some emerging techniques and toxicological issues on hazard identification for food chemicals, such as new measurement techniques, the use of transgenic animals, assessment of hormone balance and the possibilities for conducting studies in which common human diseases have been modelled, is also considered.


Subject(s)
Environmental Exposure/adverse effects , Food Analysis , Food Contamination/prevention & control , Hazardous Substances/toxicity , Models, Animal , Toxicology/methods , Animals , Food , Food Contamination/analysis , Foodborne Diseases/prevention & control , Humans , No-Observed-Adverse-Effect Level , Risk Assessment , Risk Management , Safety
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