1
vote
3answers
32 views
How best to summarise ROC score
Is there an accepted, preferably simple to calculate, number to best represent quality of a model by the position of the resulting point on a ROC diagram (true positives on y, fals …
2
votes
0answers
41 views
Convert SLN to SMARTS
Does anybody know of a tool that can convert Sybyl Line Notation queries to SMARTS queries? (Obviously Sybyl can, but I was looking for other tools)s
1
vote
1answer
44 views
Open Source Wiswesser line notation reader?
Is anyone aware of an Open Source (LGPL-compatible) algorithm for reading the Wiswesser Line Notation into a connection table? I just rediscovered Rich' nice blog about it from 200 …
1
vote
2answers
41 views
Get coordinates of beads covering the surface of a protein [closed]
Hi,
given a protein structur from the PDB, I would like to generate NS spheres of radius Rs which cover totally the protein surface. Given RS there, NS is the maximum number of sp …
1
vote
1answer
37 views
Tools for conformational clustering
Hi,
are there open source tools, for, given a set of conformations of a molecule, to cluster them into sets, being the criteria the RMSD between the confs and the parameter the RM …
0
votes
3answers
51 views
How to effectively buy compounds from ZINC database in Europe
Hi,
using virtual screening we got a list of potential interesting compounds from the ZINC database. Next we tried to buy them. For some of them, one just clicks somewhere on the …
1
vote
4answers
63 views
Chemoinformatics or cheminformatics?
What is the correct spelling, chemoinformatics or cheminformatics?
Edit: after asking the question I found some interesting web statistics by molinspiration.
2
votes
4answers
28 views
Sample Dataset for QSAR
I am interested in learning about doing QSAR. Can you recommend a sample dataset that would be a good example for learning about QSAR analysis?
0
votes
1answer
39 views
What docking tool can be easily integrated with the CDK?
I am looking for a script and/or code that calls a docking tool starting from a CDK data model. The parts I am most interested in, is how to set up the input for that docking tool …
0
votes
1answer
17 views
How can a CDK data model be saved as Gromacs input for studies it supports?
Somewhat related to the docking question, I am looking for example code for integration of the CDK and Gromacs. Can Gromacs input be auto-generated from a CDK data model for, for e …
