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Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Acta crystallographica. Section F, Structural biology communications, 2019-01, Vol.75 (1), p.19-32

2019

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On a multi-phase lag model of three-dimensional coupled thermoelasticity in an anisotropic half-space

Waves in random and complex media, 2022-07, Vol.ahead-of-print (ahead-of-print), p.1-27

2022

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Pre‐existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins

Protein science, 2011-10, Vol.20 (10), p.1645-1658

2011

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Electronic structure and microscopic charge-transport properties of a new-type diketopyrrolopyrrole-based material

Journal of computational chemistry, 2015-04, Vol.36 (10), p.695-706

2015

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NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps

Acta crystallographica. Section D, Biological crystallography., 2006-09, Vol.62 (9), p.1098-1100

2006

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DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation

Biopolymers, 2015-09, Vol.103 (9), p.528-538

2015

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The Bio3D packages for structural bioinformatics

Protein science, 2021-01, Vol.30 (1), p.20-30

2021

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SCEDS: protein fragments for molecular replacement in Phaser

Acta crystallographica. Section D, Biological crystallography., 2013-11, Vol.69 (11), p.2216-2225

2013

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Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors

FEBS letters, 2006-10, Vol.580 (22), p.5130-5136

2006

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Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables

Computational biology and chemistry, 2013-06, Vol.44, p.22-30

2013

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All-atomistic molecular dynamics study of the glass transition of amorphous polymers

Polymer (Guilford), 2022-07, Vol.254, p.125044, Article 125044

2022

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Dynamic features of homodimer interfaces calculated by normal‐mode analysis

Protein science, 2012-10, Vol.21 (10), p.1503-1513

2012

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LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor

Briefings in bioinformatics, 2020-12, Vol.21 (6), p.2206-2218

2020

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Integrating protein structural dynamics and evolutionary analysis with Bio3D

BMC bioinformatics, 2014-12, Vol.15 (1), p.399-399, Article 399

2014

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Integrative/Hybrid Modeling Approaches for Studying Biomolecules

Journal of molecular biology, 2020-04, Vol.432 (9), p.2846-2860

2020

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Layer structure and intermolecular vibrations of water confined within graphite nanoslits

Chemical physics letters, 2023-08, Vol.825, p.140612, Article 140612

2023

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Thermoelastic diffusion in nonlocal orthotropic medium with porosity

Composite structures, 2024-06, Vol.337, p.118043, Article 118043

2024

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Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins

Proteins, structure, function, and bioinformatics, 2023-10

2023

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Stability of monomeric indigo in the electronic ground state: An experimental matrix isolation infrared and theoretical study

Dyes and pigments, 2024-03, Vol.222, p.111827, Article 111827

2024

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Thermo-mechanical interactions in a nonlocal transversely isotropic material with rotation under Lord-Shulman model

Waves in random and complex media, 2024-09, Vol.34 (5), p.3970-3994

2024

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NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements

Journal of molecular biology, 2022-04, Vol.434 (7), p.167483-167483, Article 167483

2022

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Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications

Briefings in bioinformatics, 2020-05, Vol.21 (3), p.815-835

2020

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Thermo-mechanical interactions in a functionally graded orthotropic thermoelastic medium with rotation and gravity

Mechanics based design of structures and machines, 2024-07, Vol.52 (7), p.4312-4336

2024

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Generalized magneto-thermoelastic half-space with diffusion under initial stress using three-phase-lag model

Mechanics based design of structures and machines, 2017-04, Vol.45 (2), p.145-159

2017

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QuCAT: quantum circuit analyzer tool in Python

New journal of physics, 2020-01, Vol.22 (1), p.13025

2020

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Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

On a multi-phase lag model of three-dimensional coupled thermoelasticity in an anisotropic half-space

Pre‐existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins

Electronic structure and microscopic charge-transport properties of a new-type diketopyrrolopyrrole-based material

NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps

DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation

The Bio3D packages for structural bioinformatics

SCEDS: protein fragments for molecular replacement in Phaser

Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables

All-atomistic molecular dynamics study of the glass transition of amorphous polymers

Dynamic features of homodimer interfaces calculated by normal‐mode analysis

LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor

Integrating protein structural dynamics and evolutionary analysis with Bio3D

Integrative/Hybrid Modeling Approaches for Studying Biomolecules

Layer structure and intermolecular vibrations of water confined within graphite nanoslits

Thermoelastic diffusion in nonlocal orthotropic medium with porosity

Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins

Stability of monomeric indigo in the electronic ground state: An experimental matrix isolation infrared and theoretical study

Thermo-mechanical interactions in a nonlocal transversely isotropic material with rotation under Lord-Shulman model

NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements

Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications

Thermo-mechanical interactions in a functionally graded orthotropic thermoelastic medium with rotation and gravity

Generalized magneto-thermoelastic half-space with diffusion under initial stress using three-phase-lag model

QuCAT: quantum circuit analyzer tool in Python

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