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

Protein–peptide docking: opportunities and challenges

(2018) Maciej Ciemny et al.   DRUG DISCOVERY TODAY

Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold Assembly

(2018) Aleksandra E. Dawid et al.   Journal of Chemical Theory and Computation

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics

(2018) Cezary Czaplewski et al.   NUCLEIC ACIDS RESEARCH

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures

(2018) Aleksander Kuriata et al.   NUCLEIC ACIDS RESEARCH

Importance of protein flexibility on molecular recognition: modeling binding mechanisms of aminopyrazine inhibitors to Nek2

(2018) Xinyi Tang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK

(2018) Xiaotian Kong et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Generalization of the elastic network model for the study of large conformational changes in biomolecules

(2018) Adolfo B. Poma et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Protein dynamic communities from elastic network models align closely to the communities defined by molecular dynamics

(2018) Sambit Kumar Mishra et al.   PLoS One

Developing a molecular dynamics force field for both folded and disordered protein states

(2018) Paul Robustelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CABS-flex standalone: a simulation environment for fast modeling of protein flexibility

(2018) Mateusz Kurcinski et al.   BIOINFORMATICS

Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields

(2017) Parimal Kar et al.   Journal of Chemical Theory and Computation

SURPASS Low-Resolution Coarse-Grained Protein Modeling

(2017) Aleksandra E. Dawid et al.   Journal of Chemical Theory and Computation

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Toward more efficient simulations of slow processes in large biomolecular systems

(2017) Andrzej Kolinski   Physics of Life Reviews

Integrative structure modeling with the Integrative Modeling Platform

(2017) Benjamin Webb et al.   PROTEIN SCIENCE

Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information

(2017) Agnieszka S. Karczyńska et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Elastic network model of learned maintained contacts to predict protein motion

(2017) Ines Putz et al.   PLoS One

Protein Allostery and Conformational Dynamics

(2016) Jingjing Guo et al.   CHEMICAL REVIEWS

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery

(2016) Elena Papaleo et al.   CHEMICAL REVIEWS

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

New generation of elastic network models

(2016) José Ramón López-Blanco et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model

(2016) Wojciech Pulawski et al.   Journal of Chemical Information and Modeling

Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems

(2016) Albert C. Pan et al.   Journal of Chemical Theory and Computation

Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations

(2016) Ruo-Xu Gu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2016) Maciej Blaszczyk et al.   METHODS

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

(2016) Laura Orellana et al.   Nature Communications

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

(2016) Abhishek Singharoy et al.   eLife

Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction

(2016) Maciej Pawel Ciemny et al.   Scientific Reports

Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

(2015) Shoji Takada et al.   ACCOUNTS OF CHEMICAL RESEARCH

On the relationship between low-frequency normal modes and the large-scale conformational changes of proteins

(2015) Swapnil Mahajan et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Comparing the intrinsic dynamics of multiple protein structures using elastic network models

(2015) Edvin Fuglebakk et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

The anisotropic network model web server at 2015 (ANM 2.0)

(2015) E. Eyal et al.   BIOINFORMATICS

Understanding the challenges of protein flexibility in drug design

(2015) Dinler A Antunes et al.   Expert Opinion on Drug Discovery

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model

(2015) Yunjie Chen et al.   Journal of Chemical Theory and Computation

Robust elastic network model: A general modeling for precise understanding of protein dynamics

(2015) Min Hyeok Kim et al.   JOURNAL OF STRUCTURAL BIOLOGY

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

(2015) Mateusz Kurcinski et al.   NUCLEIC ACIDS RESEARCH

iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics

(2015) Hongchun Li et al.   NUCLEIC ACIDS RESEARCH

Atomic torsional modal analysis for high-resolution proteins

(2015) Monique M. Tirion et al.   PHYSICAL REVIEW E

CASP11 refinement experiments with ROSETTA

(2015) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure refinement via molecular-dynamics simulations: What works and what does not?

(2015) Michael Feig et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessing Limitations of Elastic Network Models in Describing Equilibrium Protein Flexibility and Extensions to Predict Non-Equilibrium Unfolding Dynamics of Proteins

(2015) Ravindra Venkatramani et al.   BIOPHYSICAL JOURNAL

Birth and Future of Multiscale Modeling for Macromolecular Systems (Nobel Lecture)

(2014) Michael Levitt   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture)

(2014) Arieh Warshel   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

CABS-flex predictions of protein flexibility compared with NMR ensembles

(2014) Michal Jamroz et al.   BIOINFORMATICS

Probing the Disordered Domain of the Nuclear Pore Complex through Coarse-Grained Molecular Dynamics Simulations

(2014) Ali Ghavami et al.   BIOPHYSICAL JOURNAL

Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors

(2014) Sebastian Kmiecik et al.   BIOPHYSICAL JOURNAL

Introducing Protein Intrinsic Disorder

(2014) Johnny Habchi et al.   CHEMICAL REVIEWS

A theoretical view of protein dynamics

(2014) Modesto Orozco   CHEMICAL SOCIETY REVIEWS

Integrative computational modeling of protein interactions

(2014) João P. G. L. M. Rodrigues et al.   FEBS Journal

Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations

(2014) Mateusz Kurcinski et al.   Journal of Chemical Theory and Computation

A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions

(2014) Adam Liwo et al.   JOURNAL OF MOLECULAR MODELING

iMODS: internal coordinates normal mode analysis server

(2014) José Ramón López-Blanco et al.   NUCLEIC ACIDS RESEARCH

iATTRACT: Simultaneous global and local interface optimization for protein-protein docking refinement

(2014) Christina E. M. Schindler et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

(2014) Vincent Frappier et al.   PLoS Computational Biology

Deformable elastic network refinement for low-resolution macromolecular crystallography

(2014) Gunnar F. Schröder et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

(2013) Maksim Kouza et al.   JOURNAL OF CHEMICAL PHYSICS

PRIMO: A Transferable Coarse-Grained Force Field for Proteins

(2013) Parimal Kar et al.   Journal of Chemical Theory and Computation

CABS-fold: server for the de novo and consensus-based prediction of protein structure

(2013) Maciej Blaszczyk et al.   NUCLEIC ACIDS RESEARCH

CABS-flex: server for fast simulation of protein structure fluctuations

(2013) Michal Jamroz et al.   NUCLEIC ACIDS RESEARCH

Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging

(2013) Vahid Mirjalili et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

ANM Normal Modes Show the Directions for Protein Structure Refinement

(2012) Pawel Gniewek et al.   BIOPHYSICAL JOURNAL

Coarse-grained molecular simulations of large biomolecules

(2012) Shoji Takada   CURRENT OPINION IN STRUCTURAL BIOLOGY

On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking

(2012) Matthias Dietzen et al.   Journal of Chemical Information and Modeling

Elastic network normal modes provide a basis for protein structure refinement

(2012) Pawel Gniewek et al.   JOURNAL OF CHEMICAL PHYSICS

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field

(2012) Michal Jamroz et al.   Journal of Chemical Theory and Computation

Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles

(2012) Vahid Mirjalili et al.   Journal of Chemical Theory and Computation

From Coarse-Grained to Atomic-Level Characterization of Protein Dynamics: Transition State for the Folding of B Domain of Protein A

(2012) Sebastian Kmiecik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins

(2012) D. M. Kruger et al.   NUCLEIC ACIDS RESEARCH

STRUCTURE FLUCTUATIONS AND CONFORMATIONAL CHANGES IN PROTEIN BINDING

(2012) ANATOLY M. RUVINSKY et al.   Journal of Bioinformatics and Computational Biology

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

MAVENs: Motion analysis and visualization of elastic networks and structural ensembles

(2011) Michael T Zimmermann et al.   BMC BIOINFORMATICS

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations

(2011) Phillip J. Stansfeld et al.   Journal of Chemical Theory and Computation

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

(2011) Hiroo Kenzaki et al.   Journal of Chemical Theory and Computation

Simulation of Chaperonin Effect on Protein Folding: A Shift from Nucleation–Condensation to Framework Mechanism

(2011) Sebastian Kmiecik et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model

(2010) Mustafa Tekpinar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Minimalist models for proteins: a comparative analysis

(2010) Valentina Tozzini   QUARTERLY REVIEWS OF BIOPHYSICS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Focused Functional Dynamics of Supramolecules by Use of a Mixed-Resolution Elastic Network Model

(2009) Ozge Kurkcuoglu et al.   BIOPHYSICAL JOURNAL

Coarse-Grained Description of Protein Internal Dynamics: An Optimal Strategy for Decomposing Proteins in Rigid Subunits

(2009) R. Potestio et al.   BIOPHYSICAL JOURNAL

Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

(2009) Ronald Hills et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Computational techniques for efficient conformational sampling of proteins

(2008) Adam Liwo et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Collective dynamics of the ribosomal tunnel revealed by elastic network modeling

(2008) Ozge Kurkcuoglu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes

(2008) Lei Yang et al.   STRUCTURE

Folding Pathway of the B1 Domain of Protein G Explored by Multiscale Modeling

(2007) Sebastian Kmiecik et al.   BIOPHYSICAL JOURNAL