Computational Prediction of Protein Functional Sites
Complementary computational approaches that predict functional residues in proteins by integrating sequential, structural and physiochemical features
POOL
POOL (Partial Order Optimum Likelihood) is an ML algorithm designed to identify functionally important residues in proteins, particularly those involved in catalysis or ligand binding.
GRASP-Func
GRASP-Func (Graph Representation of Active Sites for the Prediction of Function) operates by focusing on the local active site of enzymes rather than the overall fold or sequence.
POOL Analysis
Partial Order Optimum Likelihood Algorithm
POOL
Runs POOL to rank functionally important residues from input structures, producing POOL ranking files consumable by the GRASP-Func pipeline.
POOL Status
Processing your request...
POOL Instructions
- Directory Structure:
/<Protein>_<chain>.pdb - Expected Input: ZIP containing
.pdbfiles in the specified format - Expected Output: Rank file outputs for the respective proteins
GRASP-Func Analysis
Graph Representation of Active Sites for the Prediction of Function
PRE-PROCESSING
Transforms raw protein structures and ranking files from POOL into standardized formats required for functional site comparison
PROCESSING
Applies the GRASP-Func algorithm to detect, score and rank local structural matches across protein surfaces using graph-based pattern recognition
VISUALIZATION
Generates both graphical and tabular results
Preprocessing Status
Processing your request...
Processing Status
Processing your request...
Visualization Status
Processing your request...
Preprocessing Instructions
- Directory Structure:
/input/family/g* - Expected Input: ZIP file containing .pdb and .tcranks/.TICranks files named by groups (g1, g2, etc...)
- Expected Output: ZIP file containing .pdb, .rank, .qhull, .sc and .tcranks/.TICranks files
Processing Instructions
- Directory Structure:
/input/family/g* - Expected Input: ZIP file containing .pdb, .rank, .qhull, .sc and .tcranks/.TICranks files named by groups (g1, g2, etc...)
- Expected Output: ZIP file containing inter-group and intra-group matchings
Visualization Instructions
- Directory Structure: Inter-group and Intra-group matching files to be in root folder and not in nested folders
- Expected Input: ZIP file containing results_inter.txt and results_intra.txt
- Expected Output: ZIP file containing the graph visualization and the multiple alignment spreadsheet
Citations
Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties
Tong, W/, Wei, Y., Murga, L. F., Ondrechen, M. J., & Williams, R. J. · PLoS Computational Biology, 5(1), e1000266. 2009.
BibTeX
@article{tong2009partial,
title={Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties},
author={Tong, Wenxu and Wei, Ying and Murga, Leonel F and Ondrechen, Mary Jo and Williams, Ronald J},
journal={PLoS computational biology},
volume={5},
number={1},
pages={e1000266},
year={2009},
publisher={Public Library of Science San Francisco, USA}
}
Functional Classification of Protein Structures by Local Structure Matching in Graph Representation
Mills, C. L., Garg, R., Lee, J. S., Tian, L., Suciu, A., Cooperman, G. D., Beuning, P. J., & Ondrechen, M. J. · Protein Science, 27(6), 1125–1135. 2018.
BibTeX
@article{mills2018functional,
title = {Functional classification of protein structures by local structure matching in graph representation},
author = {Mills, Caitlyn L and Garg, Rohan and Lee, Joslynn S and Tian, Liang
and Suciu, Alexandru and Cooperman, Gene D and Beuning, Penny J and Ondrechen, Mary Jo},
journal = {Protein Science},
volume = {27},
number = {6},
pages = {1125--1135},
year = {2018},
publisher = {Wiley Online Library}
}
Method Paper
Citation to be added upon publication.
BibTeX
@article{PLACEHOLDER,
title = {},
author = {},
journal = {},
volume = {},
number = {},
pages = {},
year = {},
publisher = {}
}