Table 3 Arguments of virtual-screening scripts

Scoring

-f

file containing fp names

-o

output path

for each target, a list

-a

append the output file

with (fp name,

list of 50 scored lists);

-n

number of query molecules

-s

similarity measure (default: Dice)

each scored list

contains (similarity,

internal ID, active/inactive)

Validation

-m

file containing the evaluation

-o

output path

for each target,

methods and their parameters

-i

input path(s)

a dictionary of methods;

-r

file containing fingerprints to ignore

for each method,

a dictionary of fps;

for each fp, a list with

(performance value, rank)

Analysis

-o

output path

for each target, a table

-i

input path

with average performance per fp

(columns) and method (rows);

a file with average rank per fp

(columns) and method (rows);

a file with pairwise tests