Domain decomposition‐based structural condensation of large protein structures for understanding their conformational dynamics

No abstract is available for this paper.

• Publication year

  2011

• Venue

  Journal of Computational Chemistry

• Publication date

  2011-01-15

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1002/jcc.21613PMID 20645300
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Coarse-grained elastic models of protein structures for understand ing their mechanics and dynamics

  2010cited by this paper
• Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.

  2010cited by this paper
• Multiscale network model for large protein dynamics.

  2009cited by this paper
• Large Protein Dynamics Described by Hierarchical-Component Mode Synthesis.

  2009cited by this paper
• Computational Biology: New Research

  2009cited by this paper
• Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model.

  2009cited by this paper
• Mesoscopic model for mechanical characterization of biological protein materials

  2008cited by this paper
• Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes.

  2008cited by this paper
• Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements

  2008cited by this paper
• A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography

  2008cited by this paper
• Conformational transitions of adenylate kinase: switching by cracking.

  2007cited by this paper
• Coarse‐graining of protein structures for the normal mode studies

  2007cited by this paper
• Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation.

  2007cited by this paper
• Characterization of protein conformational states by normal-mode frequencies.

  2007cited by this paper
• An NMA‐guided path planning approach for computing large‐amplitude conformational changes in proteins

  2007cited by this paper
• Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES

  2006cited by this paper
• Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

  2006cited by this paper
• Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data.

  2006cited by this paper
• Normal mode analysis : theory and applications to biological and chemical systems

  2005cited by this paper
• On the Compression of Low Rank Matrices

  2005cited by this paper
• Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state.

  2005cited by this paper
• Coarse-grained normal mode analysis in structural biology.

  2005cited by this paper
• Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes.

  2005cited by this paper
• Protein structural change upon ligand binding: linear response theory.

  2005cited by this paper
• The role of shape in determining molecular motions.

  2005cited by this paper
• Collective Dynamics of Large Proteins from Mixed Coarse‐Grained Elastic Network Model

  2005cited by this paper
• Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions

  2004cited by this paper
• Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

  2003cited by this paper
• Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition.

  2003cited by this paper
• Substructure synthesis method for simulating large molecular complexes

  2002cited by this paper
• Dynamics of large proteins through hierarchical levels of coarse‐grained structures

  2002cited by this paper
• Conformational change of proteins arising from normal mode calculations.

  2001cited by this paper
• Anisotropy of fluctuation dynamics of proteins with an elastic network model.

  2001cited by this paper
• Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability

  1998cited by this paper
• Gaussian Dynamics of Folded Proteins

  1997cited by this paper
• Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis.

  1996cited by this paper
• Harmonic analysis of large systems. III. Comparison with molecular dynamics

  1995cited by this paper
• Harmonic and quasiharmonic descriptions of crambin

  1990cited by this paper
• Introduction To Modern Statistical Mechanics

  1987influential reference
• Proteins

  1987cited by this paper
• Statistical Mechanics of Elasticity

  1983cited by this paper
• Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.

  1983cited by this paper
• Computational methods in structural dynamics

  1980cited by this paper
• Analytical Methods in Vibrations

  1967cited by this paper

• Mechanical Mass-Spring Model for Understanding Globular Motion of Proteins

  2016cites this paper
• Cofilin reduces the mechanical properties of actin filaments: approach with coarse-grained methods.

  2015cites this paper
• Protein-protein interface analysis and hot spots identification for chemical ligand design.

  2014cites this paper
• Sequence-based Gaussian network model for protein dynamics

  2013cites this paper
• PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.

  2013cites this paper
• QSAR models for ACE-inhibitor activity of tri-peptides based on representation of the molecular structure by graph of atomic orbitals and SMILES

  2012cites this paper
• Rigorous coarse-graining for the dynamics of linear systems with applications to relaxation dynamics in proteins.

  2011cites this paper