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Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking

Methods (San Diego, Calif.), 2016-01, Vol.93, p.72-83

2016

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Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes

Molecules (Basel, Switzerland), 2018-08, Vol.23 (8), p.1995

2018

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Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models

International journal of molecular sciences, 2018-11, Vol.19 (11), p.3496

2018

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Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models

The Journal of chemical physics, 2015-04, Vol.142 (14), p.145104-145104

2015

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Switch from thermal to force-driven pathways of protein refolding

The Journal of chemical physics, 2017-04, Vol.146 (13), p.135101-135101

2017

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Folding Simulations of the A and B Domains of Protein G

The journal of physical chemistry. B, 2012-06, Vol.116 (23), p.6645-6653

2012

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A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain

The Journal of chemical physics, 2013-08, Vol.139 (6), p.065103-065103

2013

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Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics

International journal of molecular sciences, 2013-05, Vol.14 (5), p.9893-9905

2013

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New force replica exchange method and protein folding pathways probed by force-clamp technique

The Journal of chemical physics, 2008-01, Vol.128 (4), p.045103-045103-13

2008

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Mechanical Unfolding of Acylphosphatase Studied by Single-Molecule Force Spectroscopy and MD Simulations

Biophysical journal, 2010-07, Vol.99 (1), p.238-247

2010

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Effect of Finite Size on Cooperativity and Rates of Protein Folding

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2006-01, Vol.110 (2), p.671-676

2006

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Universal geometrical factor of protein conformations as a consequence of energy minimization

Europhysics letters, 2011-12, Vol.96 (6), p.68005

2011

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Challenges in Experimental Methods

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.281

2022

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All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.197

2022

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The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool

Methods in molecular biology (Clifton, N.J.), 2017-01, Vol.1484, p.7

2017

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Computational Models for the Study of Protein Aggregation

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.51

2022

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Contact-Based Analysis of Aggregation of Intrinsically Disordered Proteins

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.105

2022

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Aggregates Sealed by Ions

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.309

2022

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Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.175

2022

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Predictive Modeling of Neurotoxic α-Synuclein Polymorphs

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.379

2022

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Assessing the Stability of Biological Fibrils by Molecular-Scale Simulations

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.357

2022

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Molecular Dynamics Simulations of Protein Aggregation: Protocols for Simulation Setup and Analysis with Markov State Models and Transition Networks

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.235

2022

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From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.139

2022

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Modifying Amyloid Motif Aggregation Through Local Structure

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.343

2022

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Protocols for Rational Design of Protein Solubility and Aggregation Properties Using Aggrescan3D Standalone

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.17

2022

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Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking

Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes

Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models

Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models

Switch from thermal to force-driven pathways of protein refolding

Folding Simulations of the A and B Domains of Protein G

A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain

Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics

New force replica exchange method and protein folding pathways probed by force-clamp technique

Mechanical Unfolding of Acylphosphatase Studied by Single-Molecule Force Spectroscopy and MD Simulations

Effect of Finite Size on Cooperativity and Rates of Protein Folding

Universal geometrical factor of protein conformations as a consequence of energy minimization

Challenges in Experimental Methods

All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations

The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool

Computational Models for the Study of Protein Aggregation

Contact-Based Analysis of Aggregation of Intrinsically Disordered Proteins

Aggregates Sealed by Ions

Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation

Predictive Modeling of Neurotoxic α-Synuclein Polymorphs

Assessing the Stability of Biological Fibrils by Molecular-Scale Simulations

Molecular Dynamics Simulations of Protein Aggregation: Protocols for Simulation Setup and Analysis with Markov State Models and Transition Networks

From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases

Modifying Amyloid Motif Aggregation Through Local Structure

Protocols for Rational Design of Protein Solubility and Aggregation Properties Using Aggrescan3D Standalone

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