A topological approach for protein classification

Cang, Zixuan; Mu, Lin; Wu, Kedi; Opron, Kristopher; Xia, Kelin; Wei, Guo -Wei

doi:10.1515/mlbmb-2015-0009

Title: A topological approach for protein classification

Abstract

Here, protein function and dynamics are closely related to its sequence and structure. However, prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity between proteins based on protein sequence or physical information, serves as a crucial step toward the understanding of protein function and dynamics.

Authors:

Cang, Zixuan ^[1]; Mu, Lin ^[2]; Wu, Kedi ^[1]; Opron, Kristopher ^[1]; Xia, Kelin ^[1]; Wei, Guo -Wei ^[3]

Michigan State Univ., East Lansing, MI (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
The Ohio State Univ., Columbus, OH (United States)

Publication Date:: Wed Nov 04 00:00:00 EST 2015

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Org.:: USDOE Laboratory Directed Research and Development (LDRD) Program

OSTI Identifier:: 1267039

Grant/Contract Number:: AC05-00OR22725

Resource Type:: Accepted Manuscript

Journal Name:: Molecular Based Mathematical Biology

Additional Journal Information:: Journal Volume: 3; Journal Issue: 1; Journal ID: ISSN 2299-3266

Publisher:: de Gruyter

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; persistent homology; machine learning; protein classification; topological fingerprint

Citation Formats


                    Cang, Zixuan, Mu, Lin, Wu, Kedi, Opron, Kristopher, Xia, Kelin, and Wei, Guo -Wei. A topological approach for protein classification.  United States: N. p., 2015. 
Web.  doi:10.1515/mlbmb-2015-0009.

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                    Cang, Zixuan, Mu, Lin, Wu, Kedi, Opron, Kristopher, Xia, Kelin, & Wei, Guo -Wei. A topological approach for protein classification.  United States.  https://doi.org/10.1515/mlbmb-2015-0009

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                    Cang, Zixuan, Mu, Lin, Wu, Kedi, Opron, Kristopher, Xia, Kelin, and Wei, Guo -Wei. Wed .  
"A topological approach for protein classification".  United States.  https://doi.org/10.1515/mlbmb-2015-0009.  https://www.osti.gov/servlets/purl/1267039.

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@article{osti_1267039,

  title        = {A topological approach for protein classification},

  author       = {Cang, Zixuan and Mu, Lin and Wu, Kedi and Opron, Kristopher and Xia, Kelin and Wei, Guo -Wei},

  abstractNote = {Here, protein function and dynamics are closely related to its sequence and structure. However, prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity between proteins based on protein sequence or physical information, serves as a crucial step toward the understanding of protein function and dynamics.},

  doi          = {10.1515/mlbmb-2015-0009},

  journal      = {Molecular Based Mathematical Biology},

  number       = 1,

  volume       = 3,

  place        = {United States},

  year         = {Wed Nov 04 00:00:00 EST 2015},

  month        = {Wed Nov 04 00:00:00 EST 2015}

}

Copy to clipboard

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Works referenced in this record:

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Works referencing / citing this record:

On the expectation of a persistence diagram by the persistence weighted kernel
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Kusano, Genki
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Gene Coexpression Network Comparison via Persistent Homology
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Duman, Ali Nabi; Pirim, Harun
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Improved understanding of aqueous solubility modeling through topological data analysis
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Pirashvili, Mariam; Steinberg, Lee; Belchi Guillamon, Francisco
Journal of Cheminformatics, Vol. 10, Issue 1
DOI: 10.1186/s13321-018-0308-5

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Similar Records

Title: A topological approach for protein classification

Abstract

Citation Formats

The Theory of Multidimensional Persistence journal, April 2009

A Fast Learning Algorithm for Deep Belief Nets journal, July 2006

Minimal molecular surfaces and their applications journal, January 2007

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations journal, July 1983

Multivariate Data Analysis Using Persistence-Based Filtering and Topological Signatures journal, December 2012

Extending Persistence Using Poincaré and Lefschetz Duality journal, April 2008

A topological measurement of protein compressibility journal, October 2014

Extreme Elevation on a 2-Manifold journal, September 2006

Zigzag Persistence journal, April 2010

Normal vibrations of proteins: Glucagon journal, March 1982

A logical calculus of the ideas immanent in nervous activity journal, December 1943

Multiscale geometric modeling of macromolecules II: Lagrangian representation journal, June 2013

NCBI BLAST: a better web interface journal, May 2008

Topology and data journal, January 2009

A Mayer–Vietoris Formula for Persistent Homology with an Application to Shape Recognition in the Presence of Occlusions journal, September 2011

Persistent voids: a new structural metric for membrane fusion journal, May 2007

PBEQ-Solver for online visualization of electrostatic potential of biomolecules journal, May 2008

Morse Theory for Filtrations and Efficient Computation of Persistent Homology journal, July 2013

Topological Persistence and Simplification journal, November 2002

On the Local Behavior of Spaces of Natural Images journal, June 2007

Highly accurate biomolecular electrostatics in continuum dielectric environments journal, January 2007

Dynamics of a small globular protein in terms of low-frequency vibrational modes. journal, June 1983

Sliding Windows and Persistence: An Application of Topological Methods to Signal Analysis journal, May 2014

A Topological View of Unsupervised Learning from Noisy Data journal, January 2011

Variational Multiscale Models for Charge Transport journal, January 2012

I-TASSER: a unified platform for automated protein structure and function prediction journal, March 2010

Stability of Persistence Diagrams journal, December 2006

Volume data mining using 3D field topology analysis journal, January 2000

The theory of multidimensional persistence conference, January 2007

A logical calculus of the ideas immanent in nervous activity journal, January 1990

Topological persistence and simplification conference, January 2000

Stability of persistence diagrams conference, January 2005

Extreme elevation on a 2-manifold conference, January 2004

A Mayer-Vietoris formula for persistent homology with an application to shape recognition in the presence of occlusions text, January 2009

Computing multidimensional persistence text, January 2010

Persistent Cohomology and Circular Coordinates journal, March 2011

Morse Theory for Filtrations and Efficient Computation of Persistent Homology journal, July 2013

Differential Geometry Based Multiscale Models journal, February 2010

A topological measurement of protein compressibility journal, October 2014

Structural Investigation of Rimantadine Inhibition of the AM2-BM2 Chimera Channel of Influenza Viruses journal, November 2011

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential journal, June 1997

A distance for similarity classes of submanifolds of a Euclidean space journal, December 1990

Multiscale multiphysics and multidomain models—Flexibility and rigidity journal, November 2013

Dynamics of a small globular protein in terms of low-frequency vibrational modes. journal, June 1983

Persistent homology of complex networks journal, March 2009

ProFunc: a server for predicting protein function from 3D structure journal, July 2005

NCBI BLAST: a better web interface journal, May 2008

KFC Server: interactive forecasting of protein interaction hot spots journal, May 2008

Topological persistence and simplification conference, January 2000

Computing Robustness and Persistence for Images journal, November 2010

A Topological View of Unsupervised Learning from Noisy Data journal, January 2011

Describing shapes by geometrical-topological properties of real functions journal, October 2008

A Fast Learning Algorithm for Deep Belief Nets journal, July 2006

Zigzag Persistence preprint, January 2008

Sketches of a platypus: persistent homology and its algebraic foundations preprint, January 2012

Fast and Anisotropic Flexibility-Rigidity Index text, January 2014

Capturing protein multiscale thermal fluctuations preprint, January 2015

On the expectation of a persistence diagram by the persistence weighted kernel journal, July 2019

Non-empirical identification of trigger sites in heterogeneous processes using persistent homology journal, February 2018

Machine learning can be used to distinguish protein families and generate new proteins belonging to those families journal, November 2019

Gene Coexpression Network Comparison via Persistent Homology journal, September 2018

Improved understanding of aqueous solubility modeling through topological data analysis journal, November 2018

Machine Learning Algorithms for Smart Data Analysis in Internet of Things Environment: Taxonomies and Research Trends journal, January 2020

Gene Coexpression Network Comparison via Persistent Homology journal, September 2018

Improved understanding of aqueous solubility modeling through topological data analysis journal, November 2018

The Theory of Multidimensional Persistence
journal, April 2009

A Fast Learning Algorithm for Deep Belief Nets
journal, July 2006

Minimal molecular surfaces and their applications
journal, January 2007

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
journal, July 1983

Multivariate Data Analysis Using Persistence-Based Filtering and Topological Signatures
journal, December 2012

Extending Persistence Using Poincaré and Lefschetz Duality
journal, April 2008

A topological measurement of protein compressibility
journal, October 2014

Extreme Elevation on a 2-Manifold
journal, September 2006

Zigzag Persistence
journal, April 2010

Normal vibrations of proteins: Glucagon
journal, March 1982

A logical calculus of the ideas immanent in nervous activity
journal, December 1943

Multiscale geometric modeling of macromolecules II: Lagrangian representation
journal, June 2013

NCBI BLAST: a better web interface
journal, May 2008

Topology and data
journal, January 2009

A Mayer–Vietoris Formula for Persistent Homology with an Application to Shape Recognition in the Presence of Occlusions
journal, September 2011

Persistent voids: a new structural metric for membrane fusion
journal, May 2007

PBEQ-Solver for online visualization of electrostatic potential of biomolecules
journal, May 2008

Morse Theory for Filtrations and Efficient Computation of Persistent Homology
journal, July 2013

Topological Persistence and Simplification
journal, November 2002

On the Local Behavior of Spaces of Natural Images
journal, June 2007

Highly accurate biomolecular electrostatics in continuum dielectric environments
journal, January 2007

Dynamics of a small globular protein in terms of low-frequency vibrational modes.
journal, June 1983

Sliding Windows and Persistence: An Application of Topological Methods to Signal Analysis
journal, May 2014

A Topological View of Unsupervised Learning from Noisy Data
journal, January 2011

Variational Multiscale Models for Charge Transport
journal, January 2012

I-TASSER: a unified platform for automated protein structure and function prediction
journal, March 2010

Stability of Persistence Diagrams
journal, December 2006

Volume data mining using 3D field topology analysis
journal, January 2000

The theory of multidimensional persistence
conference, January 2007

A logical calculus of the ideas immanent in nervous activity
journal, January 1990

Topological persistence and simplification
conference, January 2000

Stability of persistence diagrams
conference, January 2005

Extreme elevation on a 2-manifold
conference, January 2004

A Mayer-Vietoris formula for persistent homology with an application to shape recognition in the presence of occlusions
text, January 2009

Computing multidimensional persistence
text, January 2010

Persistent Cohomology and Circular Coordinates
journal, March 2011

Morse Theory for Filtrations and Efficient Computation of Persistent Homology
journal, July 2013

Differential Geometry Based Multiscale Models
journal, February 2010

A topological measurement of protein compressibility
journal, October 2014

Structural Investigation of Rimantadine Inhibition of the AM2-BM2 Chimera Channel of Influenza Viruses
journal, November 2011

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
journal, June 1997

A distance for similarity classes of submanifolds of a Euclidean space
journal, December 1990

Multiscale multiphysics and multidomain models—Flexibility and rigidity
journal, November 2013

Dynamics of a small globular protein in terms of low-frequency vibrational modes.
journal, June 1983

Persistent homology of complex networks
journal, March 2009

ProFunc: a server for predicting protein function from 3D structure
journal, July 2005

NCBI BLAST: a better web interface
journal, May 2008

KFC Server: interactive forecasting of protein interaction hot spots
journal, May 2008

Topological persistence and simplification
conference, January 2000

Computing Robustness and Persistence for Images
journal, November 2010

A Topological View of Unsupervised Learning from Noisy Data
journal, January 2011

Describing shapes by geometrical-topological properties of real functions
journal, October 2008

A Fast Learning Algorithm for Deep Belief Nets
journal, July 2006

Zigzag Persistence
preprint, January 2008

Sketches of a platypus: persistent homology and its algebraic foundations
preprint, January 2012

Fast and Anisotropic Flexibility-Rigidity Index
text, January 2014

Capturing protein multiscale thermal fluctuations
preprint, January 2015

On the expectation of a persistence diagram by the persistence weighted kernel
journal, July 2019

Non-empirical identification of trigger sites in heterogeneous processes using persistent homology
journal, February 2018

Machine learning can be used to distinguish protein families and generate new proteins belonging to those families
journal, November 2019

Gene Coexpression Network Comparison via Persistent Homology
journal, September 2018

Improved understanding of aqueous solubility modeling through topological data analysis
journal, November 2018

Machine Learning Algorithms for Smart Data Analysis in Internet of Things Environment: Taxonomies and Research Trends
journal, January 2020

Gene Coexpression Network Comparison via Persistent Homology
journal, September 2018

Improved understanding of aqueous solubility modeling through topological data analysis
journal, November 2018