logP_prediction_template.csv

# WATER-OCTANOL (ΔG_octanol - ΔG_water) TRANSFER FREE ENERGY PREDICTIONS
#
# This file will be automatically parsed. It must contain the following four elements:
# predictions, name of method, software listing, and method description.
# These elements must be provided in the order shown with their respective headers.
#
# Any line that begins with a # is considered a comment and will be ignored when parsing.
#
# 
# PREDICTION SECTION
#
# It is mandatory to submit water to octanol (ΔG_octanol - ΔG_water) transfer free energy (TFE) predictions for all 22 molecules.
# Incomplete submissions will not be accepted.
# The energy units must be in kcal/mol.

# Please report the general molecule `ID tag` in the form of `SMXX` (e.g. SM25, SM26, etc).
# Please indicate the microstate(s) used in the `Molecule ID/IDs considered (no commas)` section (e.g. `SM25_micro000`, SM25_extra001`)
# Please report TFE standard error of the mean (SEM) and TFE model uncertainty.
#
# The data in each prediction line should be structured as follows:
# ID tag, Molecule ID/IDs considered (no commas), TFE, TFE SEM, TFE model uncertainty, (optional) logD, (optional) SEM logD
#
# Your transfer free energy prediction for the neutral form does NOT have to be `SMXX_micro000` (which is the challenge provided neutral microstate).
# If you use a microstate other than the challenge provided microstate, please fill out the `Molecule ID/IDs considered (no commas)` section using a molecule ID in the form of `SMXX_extra001` (number can vary) and please list the molecule ID and it's SMILES string in your methods description in the `METHOD DESCRIPTION SECTION`.
#
# You may optionally provide predicted logD values; these will be used as a consistency check on our estimated logD values if you submit both logP and pKa values.
#
# Only one entry in the second column (`Molecule ID/IDs considered (no commas)`) is required, but you should list all IDs considered/input to your calculations. See challenge instructions.
#
# If you have evaluated additional microstates then the molecule ID used in the `Molecule ID/IDs considered (no commas)` section needs to be in the format: `SMXX_extra001` (number can vary).
# If multiple microstates are used, please report the order of population in the aqueous phase in descending order.
# Please list microstate populations, SMILES strings and the molecule IDs in the `METHOD DESCRIPTION SECTION` section further below.
#
# The list of predictions must begin with the 'Predictions:' keyword as illustrated here.
Predictions:


#
#
# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required.
Participant name:


#
#
# Please list your organization/affiliation, using only UTF-8 characters as described above.
Participant organization:


#
#
# NAME SECTION
#
# Please provide an informal but informative name of the method used.
# The name must not exceed 40 characters.
# The 'Name:' keyword is required as shown here.
Name:


#
#
# COMPUTE TIME SECTION
#
# Please provide the average compute time across all of the molecules.
# For physical methods, report the GPU and/or CPU compute time in hours.
# For empirical methods, report the query time in hours.
# Create a new line for each processor type.
# The 'Compute time:' keyword is required as shown here.
Compute time:


#
# COMPUTING AND HARDWARE SECTION
#
# Please provide details of the computing resources that were used to train models and make predictions.
# Please specify compute time for training models and querying separately for empirical prediction methods.
# Provide a detailed description of the hardware used to run the simulations.
# The 'Computing and hardware:' keyword is required as shown here.
Computing and hardware:


# SOFTWARE SECTION
#
# List all major software packages used and their versions.
# Create a new line for each software.
# The 'Software:' keyword is required.
Software:


# METHOD CATEGORY SECTION
#
# State which method category your prediction method is better described as:
# `Physical (MM)`, `Physical (QM)`, `Empirical`, or `Mixed`.
# Pick only one category label.
# The `Category:` keyword is required.
Category:


# METHOD DESCRIPTION SECTION
#
# Methodology and computational details.
# Level of details should be roughly equivalent to that used in a publication.
# Please include the values of key parameters with units.
# Please explain how statistical uncertainties were estimated.
#
# If you have evaluated additional microstates, please report their SMILES strings and populations of all the microstates in this section.
# If you used a microstate other than the challenge provided microstate (`SMXX_micro000`), please list your chosen `Molecule ID` (in the form of `SMXX_extra001`) along with the SMILES string in your methods description.
#
# Use as many lines of text as you need.
# All text following the 'Method:' keyword will be regarded as part of your free text methods description.
Method:


#
#
# All submissions must either be ranked or non-ranked.
# Only one ranked submission per participant is allowed.
# Multiple ranked submissions from the same participant will not be judged.
# Non-ranked submissions are accepted so we can verify that they were made before the deadline.
# The "Ranked:" keyword is required, and expects a Boolean value (True/False)
Ranked: