New users

If you are new to Ligandbook have a look at the summary of Ligandbook's function and read Getting started to learn how to find parameter sets or to publish your own parameter sets on Ligandbook.

Ligandbook can be searched, either by chemical structure or by text.

Validation scores

rating meaning
1 completely unvalidated, the parameters run in a simulation, but no properties of the system have been validated
2 minimally validated, structural properties are acceptable but no explicit comparison to experiment was done
3 reasonable parameters that agree with 1-2 experimental measurements, major problems are apparent
4 strong agreement between a number of reference and computed properties, minor problems
5 perfect agreement between multiple experimental and computed values


Ligandbook is scriptable: it can return XML, JSON and YAML responces. These could be fetched inside a python script and processed. One example is text-based search – traditionally one would access.

The URL above returns a HTML page, however a tiny modification returns a YAML document

The contents of results.yml (or results.json, results.xml) can then be parsed.

$ cat results.yml
query: benzene
    - id: 659
        created_at: '2013-01-26T04:47:13+0100'
        modified_at: '2013-01-26T04:47:13+0100'
            id: 659
            name: 'Bogdan I. Iorga'
            source: 'MOL2FF ('
    - id: 660...
    - id: 661...

The parsing of YAML files can be done with PyYAML

import urllib2
import yaml

url = ""
response = urllib2.urlopen(url)