Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
IEEE/ACM Trans Comput Biol Bioinform
2019 Jan 01;164:1154-1167. doi: 10.1109/TCBB.2017.2771240.
Show Gene links
Show Anatomy links
Statistical Framework for Uncertainty Quantification in Computational Molecular Modeling.
Rasheed M
,
Clement N
,
Bhowmick A
,
Bajaj CL
.
???displayArticle.abstract???
As computational modeling, simulation, and predictions are becoming integral parts of biomedical pipelines, it behooves us to emphasize the reliability of the computational protocol. For any reported quantity of interest (QOI), one must also compute and report a measure of the uncertainty or error associated with the QOI. This is especially important in molecular modeling, since in most practical applications the inputs to the computational protocol are often noisy, incomplete, or low-resolution. Unfortunately, currently available modeling tools do not account for uncertainties and their effect on the final QOIs with sufficient rigor. We have developed a statistical framework that expresses the uncertainty of the QOI as the probability that the reported value deviates from the true value by more than some user-defined threshold. First, we provide a theoretical approach where this probability can be bounded using Azuma-Hoeffding like inequalities. Second, we approximate this probability empirically by sampling the space of uncertainties of the input and provide applications of our framework to bound uncertainties of several QOIs commonly used in molecular modeling. Finally, we also present several visualization techniques to effectively and quantitavely visualize the uncertainties: in the input, final QOIs, and also intermediate states.
Bajaj,
AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS.
2011, Pubmed
Bajaj,
AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS.
2011,
Pubmed
Bajaj,
FAST MOLECULAR SOLVATION ENERGETICS AND FORCE COMPUTATION.
2010,
Pubmed
Bashford,
Generalized born models of macromolecular solvation effects.
2000,
Pubmed
Brünger,
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures.
1992,
Pubmed
Burnley,
Modelling dynamics in protein crystal structures by ensemble refinement.
2012,
Pubmed
Case,
The Amber biomolecular simulation programs.
2005,
Pubmed
Chowdhury,
Protein-protein docking with F(2)Dock 2.0 and GB-rerank.
2013,
Pubmed
Cruickshank,
Remarks about protein structure precision.
1999,
Pubmed
Dolinsky,
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations.
2004,
Pubmed
Duan,
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
2003,
Pubmed
Eisenberg,
Solvation energy in protein folding and binding.
,
Pubmed
Emsley,
Features and development of Coot.
2010,
Pubmed
Eswar,
Comparative protein structure modeling using MODELLER.
2007,
Pubmed
Feig,
Recent advances in the development and application of implicit solvent models in biomolecule simulations.
2004,
Pubmed
Habeck,
Bayesian inference applied to macromolecular structure determination.
2005,
Pubmed
Hwang,
Protein-protein docking benchmark version 4.0.
2010,
Pubmed
Kuzmanic,
X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals.
2014,
Pubmed
Kuzmanic,
Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.
2010,
Pubmed
Lang,
Automated electron-density sampling reveals widespread conformational polymorphism in proteins.
2010,
Pubmed
Pettersen,
UCSF Chimera--a visualization system for exploratory research and analysis.
2004,
Pubmed
RAMACHANDRAN,
Stereochemistry of polypeptide chain configurations.
1963,
Pubmed
Richards,
Areas, volumes, packing and protein structure.
1977,
Pubmed
Rieping,
Inferential structure determination.
2005,
Pubmed
Touw,
BDB: databank of PDB files with consistent B-factors.
2014,
Pubmed