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Structure Class Encoding in Protein Dynamic Bioinformatics

The journal of physical chemistry. B, 2022-08, Vol.126 (31), p.5730-5734

Rackovsky, S.

2022

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The dynamic basis of structural order in proteins

Proteins, structure, function, and bioinformatics, 2022-05, Vol.90 (5), p.1115-1118

2022

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Nonlinearities in protein space limit the utility of informatics in protein biophysics

Proteins, structure, function, and bioinformatics, 2015-11, Vol.83 (11), p.1923-1928

Rackovsky, S.

2015

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Sequence determinants of protein architecture

Proteins, structure, function, and bioinformatics, 2013-10, Vol.81 (10), p.1681-1685

Rackovsky, S.

2013

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Global Survey of Protein Dynamic Properties

The journal of physical chemistry. B, 2023-07, Vol.127 (27), p.6073-6077

2023

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Sequence‐specific dynamic information in proteins

Proteins, structure, function, and bioinformatics, 2019-10, Vol.87 (10), p.799-804

2019

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Spectral analysis of a protein conformational switch

Physical review letters, 2011-06, Vol.106 (24), p.248101-248101, Article 248101

Rackovsky, S

2011

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The structure of protein dynamic space

Proceedings of the National Academy of Sciences - PNAS, 2020-08, Vol.117 (33), p.19938-19942

2020

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Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences

Proteins, structure, function, and bioinformatics, 2024-05, Vol.92 (10), p.1234-1241

2024

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Global informatics and physical property selection in protein sequences

Proceedings of the National Academy of Sciences - PNAS, 2016-02, Vol.113 (7), p.1808-1810

2016

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Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences

Proceedings of the National Academy of Sciences - PNAS, 2014-04, Vol.111 (14), p.5225-5229

2014

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Global characteristics of protein sequences and their implications

Proceedings of the National Academy of Sciences - PNAS, 2010-05, Vol.107 (19), p.8623-8626

Rackovsky, S

2010

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Alternative approach to protein structure prediction based on sequential similarity of physical properties

Proceedings of the National Academy of Sciences - PNAS, 2015-04, Vol.112 (16), p.5029-5032

2015

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Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins

Proceedings of the National Academy of Sciences - PNAS, 2017-02, Vol.114 (7), p.1578-1583

2017

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Characterization of Architecture Signals in Proteins

The journal of physical chemistry. B, 2006-09, Vol.110 (38), p.18771-18778

Rackovsky, S

2006

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Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States

Journal of chemical theory and computation, 2013-10, Vol.9 (10), p.4620-4632

2013

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Beyond supersecondary structure: the global properties of protein sequences

Methods in molecular biology (Clifton, N.J.), 2013, Vol.932, p.107

Rackovsky, S

2013

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New optimization method for conformational energy calculations on polypeptides: Conformational space annealing

Journal of computational chemistry, 1997-07, Vol.18 (9), p.1222-1232

1997

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Information and discrimination in pairwise contact potentials

Proteins, structure, function, and bioinformatics, 2008-05, Vol.71 (3), p.1071-1087

2008

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"Hidden" Sequence Periodicities and Protein Architecture

Proceedings of the National Academy of Sciences - PNAS, 1998-07, Vol.95 (15), p.8580-8584

Rackovsky, S.

1998

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Improvement of statistical potentials and threading score functions using information maximization

Proteins, structure, function, and bioinformatics, 2006-03, Vol.62 (4), p.892-908

2006

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On the information content of protein sequences

Journal of biomolecular structure & dynamics, 2011-02, Vol.28 (4), p.593-594

2011

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On the properties and sequence context of structurally ambivalent fragments in proteins

Protein science, 2003-11, Vol.12 (11), p.2420-2433

2003

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A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data

Journal of computational chemistry, 1997-05, Vol.18 (7), p.849-873

1997

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Property-based sequence representations do not adequately encode local protein folding information

Proteins, structure, function, and bioinformatics, 2007-06, Vol.67 (4), p.785-788

2007

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Structure Class Encoding in Protein Dynamic Bioinformatics

The dynamic basis of structural order in proteins

Nonlinearities in protein space limit the utility of informatics in protein biophysics

Sequence determinants of protein architecture

Global Survey of Protein Dynamic Properties

Sequence‐specific dynamic information in proteins

Spectral analysis of a protein conformational switch

The structure of protein dynamic space

Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences

Global informatics and physical property selection in protein sequences

Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences

Global characteristics of protein sequences and their implications

Alternative approach to protein structure prediction based on sequential similarity of physical properties

Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins

Characterization of Architecture Signals in Proteins

Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States

Beyond supersecondary structure: the global properties of protein sequences

New optimization method for conformational energy calculations on polypeptides: Conformational space annealing

Information and discrimination in pairwise contact potentials

"Hidden" Sequence Periodicities and Protein Architecture

Improvement of statistical potentials and threading score functions using information maximization

On the information content of protein sequences

On the properties and sequence context of structurally ambivalent fragments in proteins

A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data

Property-based sequence representations do not adequately encode local protein folding information

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