hERG – Prediction of cardiotoxicity of drugs

By | September 22, 2011

INTRODUCTION

This Web Service implements hERG 1.0. It predicts cardiotoxicity of drug
molecules. The method is described in detail in the following article:

hERG Classification Model Based on a Combination of Support Vector Machine
Method and GRIND Descriptors.
Li Q, Joergensen FS, Oprea T, Brunak S, Taboureau O.
Mol Pharm: 4;5:117-127, 2008.

Alongside this Web Service the hERG method is also implemented as
a traditional paste-and-click WWW server at:

http://www.cbs.dtu.dk/services/hERG-1.0/

The traditional server offers extended functionality and comprehensive
documentation. It is suitable for close investigation of few molecules;
this service is recommended for high throughput projects.

TECHNICAL NOTE

The main output data type ‘anndata’ is reused from biological sequence
analysis where it normally contains protein or nucleotide sequences annotations.
This Web Service, however, is about molecules, not sequences. Therefore,
the names of the tags e.g. ‘sequence’ might seem misleading. We have
chosen to reuse some data types anyway as they have proved very versatile.

WEB SERVICE OPERATION

This Web Service is fully asynchronous; the usage is split into the
following three operations:

1. runService

Input: The following parameters and data:

* sort sort the output by predicted cardiotoxicity
(no value, just presence/absence);

* moleculedata mulitple elements of type ‘molecule’:
* molecule answers to one molecule:
* id unique identifier for the molecule
* comment optional comment (ignored by this service)
* smiles molecule description string in SMI format

Output: Unique job identifier

2. pollQueue

Input: Unique job identifier

Output: ‘jobstatus’ – the status of the job
Possible values are QUEUED, ACTIVE, FINISHED, WAITING,
REJECTED, UNKNOWN JOBID or QUEUE DOWN

3. fetchResult

Input: Unique job identifier of a FINISHED job

Output: * ‘annsource’
‘method’ name of the method, here always ‘hERG’;
‘version’ version of the method: here always 1.0c;

‘ann’ annotations – one element per input molecule
‘sequence’ standard sequence object (reused for molecules)
‘id’ molecule identifier
‘annrecords/annrecord’
‘feature’ feature name, here always ‘hERG’;
‘global’ always present, indicates the whole molecule
‘score’
‘key’ here always: main
‘value’ score value
‘comment’ answer: high, low or ‘-’
CONTACT

Questions concerning the scientific aspects of the hERG method should
go to Olivier Taboureau, otab@cbs.dtu.dk; technical questions concerning
the Web Service should go to Edita Bartaseviciute, edita@cbs.dtu.dk or
Kristoffer Rapacki, rapacki@cbs.dtu.dk.

Name
hERG – Prediction of cardiotoxicity of drugs
Documentation
http://www.cbs.dtu.dk/services/hERG-1.0/
Protocol
SOAP
WSDL
Endpoint
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/quasi-1.2c.cgi?log
Topic
Biology
Type
Tags
, , ,
Description

INTRODUCTION This Web Service implements hERG 1.0. It predicts cardiotoxicity of drug molecules. The method is described in detail in [...]

Further information

INTRODUCTION

This Web Service implements hERG 1.0. It predicts cardiotoxicity of drug
molecules. The method is described in detail in the following article:

hERG Classification Model Based on a Combination of Support Vector Machine
Method and GRIND Descriptors.
Li Q, Joergensen FS, Oprea T, Brunak S, Taboureau O.
Mol Pharm: 4;5:117-127, 2008.

Alongside this Web Service the hERG method is also implemented as
a traditional paste-and-click WWW server at:

http://www.cbs.dtu.dk/services/hERG-1.0/

The traditional server offers extended functionality and comprehensive
documentation. It is suitable for close investigation of few molecules;
this service is recommended for high throughput projects.

TECHNICAL NOTE

The main output data type ‘anndata’ is reused from biological sequence
analysis where it normally contains protein or nucleotide sequences annotations.
This Web Service, however, is about molecules, not sequences. Therefore,
the names of the tags e.g. ‘sequence’ might seem misleading. We have
chosen to reuse some data types anyway as they have proved very versatile.

WEB SERVICE OPERATION

This Web Service is fully asynchronous; the usage is split into the
following three operations:

1. runService

Input: The following parameters and data:

* sort sort the output by predicted cardiotoxicity
(no value, just presence/absence);

* moleculedata mulitple elements of type ‘molecule’:
* molecule answers to one molecule:
* id unique identifier for the molecule
* comment optional comment (ignored by this service)
* smiles molecule description string in SMI format

Output: Unique job identifier

2. pollQueue

Input: Unique job identifier

Output: ‘jobstatus’ – the status of the job
Possible values are QUEUED, ACTIVE, FINISHED, WAITING,
REJECTED, UNKNOWN JOBID or QUEUE DOWN

3. fetchResult

Input: Unique job identifier of a FINISHED job

Output: * ‘annsource’
‘method’ name of the method, here always ‘hERG’;
‘version’ version of the method: here always 1.0c;

‘ann’ annotations – one element per input molecule
‘sequence’ standard sequence object (reused for molecules)
‘id’ molecule identifier
‘annrecords/annrecord’
‘feature’ feature name, here always ‘hERG’;
‘global’ always present, indicates the whole molecule
‘score’
‘key’ here always: main
‘value’ score value
‘comment’ answer: high, low or ‘-’
CONTACT

Questions concerning the scientific aspects of the hERG method should
go to Olivier Taboureau, otab@cbs.dtu.dk; technical questions concerning
the Web Service should go to Edita Bartaseviciute, edita@cbs.dtu.dk or
Kristoffer Rapacki, rapacki@cbs.dtu.dk.

Original source
BioCatalogue

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