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MetaDrug & MetabolExpert

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Автор темы

Кто-нибудь пользовался данными программами? Если да, то какие впечатления от софта? Есть ли у кого-нибудь доступ к данным программам? Очень нужна помощь в расчете конечных метаболитов 3-6 структур.

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Автор темы

Антон Мымриков, лично я на такие продукты не натыкался, но меня терзают смутные сомнения в отношении существования оных.

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Dimitrius, спасибо за интересную информацию. Лично никогда не работал и даже не знал про этот софт, но теперь обращу на него внимание.
Я так понял, что он предназначен для расчетов параметров метаболитов? QSAR только "узкозаточенный"?
Может быть напишете об этих софтинках подробнее?

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Автор темы

Вот что по этим программам есть:

MetaDrug
Compound Based Pathway Analysis, Systems Pharmacology & Chemical Biology
MetaDrug™ is a unique systems pharmacology platform designed for evaluation of biological effects of small molecule compounds on the human body, with pathway analysis and other bioinformatics applications from toxicogenomics to translational medicine. MetaDrug™ helps to solve such problems as drug’s mechanism of action, toxicity and off-target effects, deduced from the structure and any kind of supplementary toxicogenomics data. The product is intended to be used by medicinal chemists and biologists active in pre-clinical areas of high content and high throughput screening, bioassays, hit-to-lead libraries, lead optimization, PK and toxicogenomics, with the eventual goal being practical applications in translational medicine and more
Product highlights
Evaluates potential indications, off-target effects, mechanism of action, toxicity starting with structures or OMICs data
Compares and ranks up to 1,000 compounds based on toxic effects, therapeutic activity, affected targets and pathways
Predicts human metabolites based on empirical rules
Contains over 70 QSAR models for activity, toxicity and metabolism. Builds custom QSAR models
Works on a manually curated database of over 600,000 biologically active compounds; 65,000 human, mice and rat proteins and over 500,000 protein-compound interactions
Applications
Drug repositioning
Compound prioritization and library triage
Compound profiling
Hit-to-lead optimization
Drug comparison to competitor’s
Toxicogenomics studies
Biological effects of new compounds
Evaluation of potential indications, off-target effects, mechanism of action and toxicity starting from chemical structure
Prediction of targets based on similarity search through 600,000 bioactive chemistry space in GeneGo database and portfolio of QSAR models
Ranking and prioritization of cellular pathways, biological processes, toxic categories, diseases most likely to be affected by your compounds
Comparison and prioritization of up to 1,000 compounds based on biological effects and toxicity
Manually curated networks for diseases, toxicogenomics categories and cellular processes
Compound-centered networks and interpretation for translational medicine
Parsers for individual and batch structures in MOL, CDX or SD file format (up to 1,000 compounds)
Data export to Excel for SAR table views
Toxicogenomics predictive features
Rule-based prediction of major human phase I and II metabolites
Over 70 QSAR models for drug metabolizing enzymes, major safety and toxicity targets and general toxic categories
Multidimensional compound filtering using adjustable QSAR models thresholds
Manually created networks for toxic and xenobiotic metabolism categories
Automated toxicogenomics workflow for OMICs data analysis in context of different organs
Features for network and pathway analysis of accompanying OMICs data
Parsers for microarray gene expression, proteomics, siRNA screens, metabolomics and other high-throughput data
Functional analysis of OMICs data to show most relevant cellular pathways, biological processes, toxic categories and diseases
Concurrent visualization of multiple data types: metabolomic and microarray, SNP and metabolic etc
One-button comparison of toxicogenomics and drug effect gene expression profiles
Reporting of pathway analysis results to Excel
Multiple network generating algorithms, intuitive pathway editing and visualization tools
Content
Unique manually curated database on activity of 600,000 compounds in binding, functional, and ADMETox assays
Tens of thousands of human xenobiotic reactions with metabolizing enzymes and kinetic data
All marketed and clinical trial drugs with targets and downstream signaling
Comprehensive coverage of compound-protein interactions from peer-reviewed literature and patents with IC50 and Ki data
Custom QSAR modeling. Users can include their own proprietary data and “chemistry space” into MetaDrug analysis
Unique pathway maps for diseases, toxicities and drug effects for use in translational medicine, toxicogenomics, etc.
Seamless integration with Sigma Aldrich web site to purchase compounds and Symyx’s DiscoveryGate family of databases to search for additional information
System design
Unique Oracle-based database architecture
Compatibility with pharmaceutical IT infrastructure for lead prioritization and comprehensive toxicogenomics studies
Seamlessly integrated with MetaCore™, MetaRodent, MapEditor™ and MetaLink™ for a robust bioinformatics solution dedicated to pathway analysis and toxicogenomics research
Server-client architecture

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MetabolExpert
Customer Benefits

MetabolExpert is an ideal program for a quick prediction of the metabolic fate of a compound in the drug discovery process or during the dispositional research phase. It also helps the analysis of metabolic experiments.

Brief Description

CompuDrug's MetabolExpert is a unique tool for initial estimation of the structural formula of metabolites, which might be formed by a substance in humans, animals or in plants. MetabolExpert is a rule-based system with open architecture, in other words, the chemists, metabolism researchers, drug disposition experts and environmental managers can understand, expand, modify or optimize the data on which the metabolic structural estimation relies. The input of the structural transformation is facilitated by an easy-to-use graphical interface, and the metabolic tree graph is displayed in a way that is especially suitable for reporting..

Features at a Glance
Predicts the most common metabolic pathways in animals, plants or through photodegradation
Metabolites are collected in compound databases
Results are presented in metabolic tree format (reporting viewing)
Graphical interface for editing transformation rules
Open knowledge bases - user can add own rules
Exporting results to SDF and RDF format
Graphical highlighting empasizes the essence of metabolic reactions that occurred

MetabolExpert upgrade

The knowledge base of the MetabolExpert module of Pallas has been extended with new metabolic reactions. The extension includes a set of special metabolic reactions collected from the scientific literature focusing on the metabolisms of toxic and drug-like organic compounds. Thanks to the inserted reactions, the new version of MetabolExpert will manage a series of special metabolisms, including ring opening and closing reactions.

Информация взята с оф. сайтов. Но очень хотелось бы проверить данные программы в действии на своих веществах. Наткнулся чисто случайно в поисках информации.

QSAR только "узкозаточенный"?

Да. Очень на то похоже.

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Dimitrius, не совсем понял, программы работают сугубо с теоретическими и модельными данными или можно и эмпирические закладывать для обработки и сравнения?

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Автор темы

Антон Мымриков, копавшись в инете, натыкался на информацию, что можно "обучать", что расширяет горизонты их применения.

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С QSAR не работал никогда, только на теоретическом уровне интересовался. Вот если бы эти штуки еще и фармакокинетику моделировали, пожалуй взялся бы их поковырять... Для меня была бы очень интересна такая последовательность:
Взять субстанцию -> Сделать прогноз возможных метаболитов -> Просчитать их возможные фармакологические эффекты и активность по отношению к начальной субстанции -> Смоделировать ФК данных метаболитов. Есть что-либо, что умеет делать подобное?

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