Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis
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journal
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August 1996 |
Generic Rigidity Percolation: The Pebble Game
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journal
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November 1995 |
iMod: multipurpose normal mode analysis in internal coordinates
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journal
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August 2011 |
A Method of Rapid Calculation of a Second Derivative Matrix of Conformational Energy for Large Molecules
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journal
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October 1983 |
Atomic torsional modal analysis for high-resolution proteins
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journal
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March 2015 |
A new approach for determining low-frequency normal modes in macromolecules
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journal
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June 1994 |
Building-block approach for determining low-frequency normal modes of macromolecules
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journal
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January 2000 |
ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
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journal
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July 2004 |
Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
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journal
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February 1985 |
Conventional NMA as a better standard for evaluating elastic network models: NMA as a Better Standard for Evaluating ENMs
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journal
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December 2014 |
Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models
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journal
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October 2015 |
Functional Modes of Proteins Are among the Most Robust
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journal
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February 2006 |
Torsional Network Model: Normal Modes in Torsion Angle Space Better Correlate with Conformation Changes in Proteins
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journal
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June 2010 |
Optimized Torsion-Angle Normal Modes Reproduce Conformational Changes More Accurately Than Cartesian Modes
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journal
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December 2011 |
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
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journal
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June 1997 |
Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model
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journal
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January 1998 |
Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model
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journal
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January 2001 |
An Algorithm for Two-Dimensional Rigidity Percolation: The Pebble Game
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journal
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November 1997 |
Protein flexibility and dynamics using constraint theory
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journal
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February 2001 |
Generic rigidity in three-dimensional bond-bending networks
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journal
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August 1998 |
Counting out to the flexibility of molecules
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journal
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November 2005 |
A proof of the molecular conjecture
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conference
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January 2009 |
KINARI-Web: a server for protein rigidity analysis
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journal
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June 2011 |
Floppy modes in network glasses
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journal
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November 1989 |
Algorithms for three-dimensional rigidity analysis and a first-order percolation transition
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journal
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October 2007 |
Protein flexibility predictions using graph theory
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journal
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January 2001 |
Global and local indices for characterizing biomolecular flexibility and rigidity
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journal
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September 2012 |
Protein unfolding: Rigidity lost
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journal
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March 2002 |
Analyzing the Flexibility of RNA Structures by Constraint Counting
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journal
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June 2008 |
Detecting the native ligand orientation by interfacial rigidity: SiteInterlock: Identifying Ligand Binding Poses by Rigidity
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journal
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October 2016 |
Nonadditivity in Conformational Entropy upon Molecular Rigidification Reveals a Universal Mechanism Affecting Folding Cooperativity
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journal
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February 2011 |
Rigidity Theory-Based Approximation of Vibrational Entropy Changes upon Binding to Biomolecules
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journal
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March 2017 |
Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations
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journal
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January 2017 |
Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods
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journal
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January 2018 |
Simulating Protein Motions with Rigidity Analysis
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journal
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July 2007 |
Multi-Resolution Rigidity-Based Sampling of Protein Conformational Paths
- Luo, Dong; Haspel, Nurit
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BCB'13: ACM-BCB2013, Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
https://doi.org/10.1145/2506583.2506710
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conference
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September 2013 |
Thermostability in rubredoxin and its relationship to mechanical rigidity
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journal
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December 2009 |
Protein rigidity and thermophilic adaptation
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journal
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January 2011 |
Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis
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journal
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March 2016 |
Identifying protein folding cores from the evolution of flexible regions during unfolding
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journal
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December 2002 |
Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family
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journal
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August 2008 |
Sampling protein conformations and pathways
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journal
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January 2004 |
Constrained geometric simulation of diffusive motion in proteins
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journal
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November 2005 |
Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory
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journal
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February 2006 |
Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses
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journal
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February 2012 |
Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations
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journal
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October 2015 |
Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs
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journal
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July 2015 |
Coupled Motions in β 2 AR:Gαs Conformational Ensembles
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journal
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February 2016 |
Elasticity, strength and resilience: A comparative study on mechanical signatures of α-Helix, β-sheet and tropocollagen domains
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journal
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July 2008 |
Automated design of the surface positions of protein helices: Protein surface design
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journal
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June 1997 |
Accessible Surfaces of Beta Proteins Increase with Increasing Protein Molecular Mass More Rapidly than Those of Other Proteins
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journal
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December 2011 |
How soft is a single protein? The stress–strain curve of antibody pentamers with 5 pN and 50 pm resolutions
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journal
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January 2016 |
Collective protein dynamics and nuclear spin relaxation
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journal
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February 1995 |
Accurate de novo design of hyperstable constrained peptides
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journal
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September 2016 |
Universality of vibrational spectra of globular proteins
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journal
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February 2016 |
Geometric Confinement Governs the Rupture Strength of H-bond Assemblies at a Critical Length Scale
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journal
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February 2008 |
Adenylate Kinase and AMP Signaling Networks: Metabolic Monitoring, Signal Communication and Body Energy Sensing
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journal
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April 2009 |
Induced-fit movements in adenylate kinases
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journal
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June 1990 |
Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution
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journal
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March 1992 |
Domain Closure in Adenylate Kinase
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journal
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January 1993 |
Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
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journal
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May 1995 |
Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding
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journal
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February 1996 |
Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open↔Closed Transitions
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journal
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November 2009 |
Sampling large conformational transitions: adenylate kinase as a testing ground
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journal
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May 2014 |
Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case
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journal
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August 2015 |
Frustration-guided motion planning reveals conformational transitions in proteins: BUDDAY et al.
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journal
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July 2017 |
Direct observation of ultrafast large-scale dynamics of an enzyme under turnover conditions
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journal
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March 2018 |
Fast, clash-free RNA conformational morphing using molecular junctions
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journal
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March 2017 |
Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces
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journal
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January 2018 |
Hydrogen bonds are a primary driving force for de novo protein folding
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journal
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November 2017 |
Intermolecular hydrogen bonding strategy to fabricate mechanically strong hydrogels with high elasticity and fatigue resistance
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journal
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January 2013 |
A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds
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journal
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November 2012 |
The coming of age of de novo protein design
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journal
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September 2016 |
De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity
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journal
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May 2016 |
Integrative, dynamic structural biology at atomic resolution—it's about time
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journal
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March 2015 |
Entropic Elasticity Controls Nanomechanics of Single Tropocollagen Molecules
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journal
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July 2007 |
Low-frequency modes in the Raman spectra of proteins
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journal
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July 1982 |
A Distinct Utility of the Amide III Infrared Band for Secondary Structure Estimation of Aqueous Protein Solutions Using Partial Least Squares Methods †
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journal
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March 2004 |
Obtaining information about protein secondary structures in aqueous solution using Fourier transform IR spectroscopy
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journal
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February 2015 |
Mechanical Response of Silk Crystalline Units from Force-Distribution Analysis
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journal
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May 2009 |
Hydration Water Dynamics Near Biological Interfaces
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journal
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December 2008 |
A unified model of protein dynamics
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journal
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February 2009 |