Marvin Live Plugin Catalogue

Realtime plugins

Name

Description

Required ChemAxon licenses

Min CPU
(cores)

Min memory
(GB)

Supports
user settings

Communication method

Service location

Security

Request format

Molecule format conversion required

Response format

Returned data

Supports reported data

Alignment RCSB.org

Calculates overlay of idea vs pre-docked ligand. Displays results in binding site.

JChem Web Services, Structural Calculations

8

4

Yes

HTTP

internal + external

SSL

JSON

No

JSON

3D

No

Alignment (local/ftp)

Same as above, but protein is fetched from an internal server, not rcsb.org.

JChem Web Services, Structural Calculations

8

4

Yes

HTTP

internal + external

SSL

JSON

No

JSON

3D

No

Alignment (Lambda + S3)

Same as above, but protein is fetched from S3 folder, and the calculation is run using a Lambda function.

Structural Calculations

8

4

Yes

HTTP

internal + external

token

JSON

No

JSON

3D

No

Alignment RCSB.org (RDKit)

Same as above, but overlay is calculated with RDKit.

RDKit

8

4

Yes

Command Line

internal

none

JSON

Yes - SMILES

JSON

3D

No

Calculated Properties

Runs basic med-chem property predictors.

JChem Web Services, all calculators

4

4

N - can be added

HTTP

internal + external

SSL

JSON

No

JSON

list of numbers

Yes

ChEMBL

Returns molecules and activity values from chembl (sim search, high p_chembl value).

JChem Web Services

1

N - can be added

HTTP

external

none

JSON

Yes - SMILES

JSON

molecules, images, numbers

Yes

MyChEMBL

Same as above, but using the MyChEMBL local VM.

JChem Web Services

1

N - can be added

HTTP

internal

none

JSON

Yes - SMILES

JSON

molecules, images, numbers

Yes

Conformers

Generates lowest energy conformer of a molecule with ChemAxon 3D Alignment

JChem Web Services, Structural Calculations

4

N - can be added

HTTP

internal

SSL

JSON

No

JSON

3D

Yes

Conformers

Generates lowest energy conformer of a molecule with RDKit algorithm.

RDKit

4

N - can be added

Command Line

internal

none

JSON

Yes - SMILES

JSON

3D

Yes

PubChem

Returns substructure matches through PubChem's PUG interface

1

N - can be added

HTTP

external

none

URL

Yes - SMILES

JSON

molecules, images, numbers

Yes

Compliance Checker

Fetches legislative references for a molecule

Compliance Checker

4

4

N - can be added

HTTP

internal

SSL

JSON

No

JSON

list of links

Yes

CRAIS Checker

Fetches legislative references for a molecule

CRAIS Checker

4

4

N - can be added

HTTP / SOAP

internal

cookie

XML

No

XML

list of links

Yes

Compound Registration

Checks a molecule in the corporate registry and returns its ID

Compound Registration

4

4

N - can be added

HTTP

internal

token + cookie

JSON

No

JSON

molecules, images, IDs

Yes

DrugBank

Checks a molecule in DrugBank and returns the closest match

JChem Base

1

N - can be added

HTTP

external

SSL

JSON

No

JSON

molecules, images, IDs

Yes

eMolecules

Runs screening compound and starting material search in eMolecules

1

Yes

HTTP / SOAP

external

token

XML

Yes - SMILES

XML

molecules, images, IDs

Yes

eMolecules (local)

Same as above, but uses local ChemAxon Postgres Cartridge for searching

JChem Postgres Cartridge

8

32

Yes

SQL

internal

SSL

SQL query

No

SQL resultset

molecules, images, IDs

Yes

HERG assistant

Return suggested transformations to reduce hERG liability using MMP knowledge base

JChem Web Services, Structure Checker

1

1

N - can be added

HTTP

internal

SSL

JSON

No

JSON

list of numbers

Yes

SureChEMBL

Runs similarity search across SureChEMBL

Madfast Similarity Search

4

8

Yes

HTTP

internal

SSL

JSON

No

JSON

molecules, images, IDs

Yes

Enamine REAL

Runs similarity search across the Enamine REAL database

Madfast Similarity Search

16

128

Yes

HTTP

internal

SSL

JSON

No

JSON

molecules, images, IDs

Yes

Enamine Store

Run searches in the Enamine Store SCR and BB catalog

Yes

HTTP

internal

SSL

URL

Yes - SMILES

JSON

molecules, IDs

Yes

MolPort

Runs screening compound and starting material search in Molport

1

Yes

HTTP

internal

token

JSON

Yes - SMILES

JSON

molecules, images, IDs

Yes

Atom economny

Calculates the atom economy of the reaction

N - can be added

HTTP

internal

SSL

JSON

No

JSON

list of numbers

No

Carbon Efficiency

Calculates the carbon efficiency of the reaction

N - can be added

HTTP

internal

SSL

JSON

No

JSON

list of numbers

No

Patented Reactions

Searches in a patent database of reactions and returns the best match

JChem Base

N - can be added

HTTP

internal

SSL

JSON

No

JSON

reactions, images, IDs

No

UniChem

Runs duplicate search in UniChem and returns database IDs

1

N - can be added

HTTP

external

SSL

URL

Yes - InChi Key

JSON

list of links

Yes

Reaxys

Runs search in Reaxys and returns compound information and citations

1

N - can be added

HTTP / XML

external

IP + cookie

XML

Yes - Molfile

XML

molecules, images, IDs

Yes

ligprep

Checks the structure with typical rules used by compchems

Pipeline Pilot Components, all calculators

4

N - can be added

HTTP

internal

SSL

JSON

No

JSON

molecules, text

Yes

sweet spot analysis

Displays a gradient colored scatter plot of mass and logd values

JChem Web Services, Structural Calculations, Partitioning, Protonation

4

4

N - can be added

HTTP

internal

none

JSON

No

JSON

scatter plot

Yes

CNS MPO

Calculates and displays a radar plot of Pfizer CNS MPO scoring

JChem Web Services, all calculators

4

4

N - can be added

HTTP

internal

none

JSON

No

JSON

list of numbers, radar chart

Yes

logD chart

Calculates the displays a pH-logD chart

JChem Web Services, Structural Calculations, Partitioning

2

2

N - can be added

HTTP

internal

none

JSON

No

JSON

list of numbers, line chart

Yes

Zinc natural derivates

Returns substructure matches from select Zinc subsets

JChem Postgres Cartridge

4

4

Yes

SQL

internal

SSL

SQL query

No

SQL resultset

molecules, images, IDs

Yes

Virtual registry search

Searches the registered ideas in the idea collection while in a design session

Compound Registration

2

4

Yes

HTTP

internal

token + cookie

JSON

No

JSON

molecules, images, IDs

No

MCule

Runs exact match searches in the MCule online catalog

JChem Web Services

N - can be added

HTTP

external

SSL

URL

Yes - SMILES

JSON

molecules, IDs, text

No

Structure Checker

Checks drawing quality of molecules and offers fixing them

JChem Web Services, Structure Checker

1

2

Yes

HTTP

internal

SSL

JSON

No

JSON

molecules, text

Yes

Structural Alerts

Checks substructure patterns in a molecule like REOS, PAINS, toxiphores

JChem Web Services, Structure Checker

1

0

Yes

HTTP

internal

SSL

JSON

No

JSON

text, images

Yes

ChemLocator

Finds relevant documents based on matching chemical structures in a ChemLocator index

ChemLocator

2

8

Yes

HTTP

internal

SSL

JSON

No

JSON

molexules, images, text

Yes

Toxpredict

Runs toxtree predictions using toxpredict.net

N - can be added

HTTP

external

SSL

JSON

Yes - SMILES

JSON

IDs, text

No

Resolver Plugins

Name

Description

Required ChemAxon licenses

Min CPU
(cores)

Min memory
(GB)

Supports
user settings

Communication method

Service location

Security

Request format

Molecule format conversion required

Response format

Returned data

Supports reported data

Corporate IDs

Returns the molecule for a given ID using a custom dictionary

JChem Web Services, Name to Structure

1

HTTP

internal

SSL

No

JSON

Compound IDs

Returns the molecule for a given ID using Compound Registration

Compound Registration

1

HTTP

internal

token + cookie

No

JSON

Exporter Plugins

Name

Description

Required ChemAxon licenses

Min CPU
(cores)

Min memory
(GB)

Supports
user settings

Communication method

Service location

Security

Request format

Molecule format conversion required

Response format

Returned data

Supports reported data

Compound Registry

Registers the selected ideas

Compound Registration

2

4

HTTP

internal

token + cookie

No

JSON

ELN experiment

Creates an experiment draft in the ELN with the specified compound in IDBS E-Workbook

8

4

HTTP

internal

cookie

JSON

No

JSON

Storage Plugins

Name

Description

Required ChemAxon licenses

Min CPU
(cores)

Min memory
(GB)

Supports
user settings

Communication method

Service location

Security

Request format

Molecule format conversion required

Response format

Returned data

Supports reported data

postgres storage

Automatically creates backup of snapshots and metadata in a project database

JChem Web Services, Structural Calculations

SQL

internal

SSL

SQL Query

Yes - Molfile

jchem postgres storage

automatically creates backup of snapshots and metadata in a project database

JChem Postgres Cartridge

SQL

internal

SSL

SQL Query

No

oracle storage

Automatically creates backup of snapshots and metadata in a project database

JChem Oracle Cartridge

SQL

internal

SSL

SQL Query

Yes - Molfile

jchem oracle storage

Automatically creates backup of snapshots and metadata in a project database

JChem Oracle Cartridge

SQL

internal

SSL

SQL Query

No

mysql storage

Automatically creates backup of snapshots and metadata in a project database

SQL

internal

SSL

SQL Query

Yes - Molfile

web services storage

Automatically creates backup of snapshots and metadata in a project database

JChem Web Services

SQL

internal

SSL

SQL Query

No

Virtual registry storage

Registers snapshots in the compound registration and assigns a unique ID

Compound Registration

2

4

HTTP

internal

token + cookie

JSON

No

JSON