Network representation of protein interactions: Theory of graph description and analysis

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Protein Science

• Publication date

  2016-09-01

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1002/pro.2963PMID 27272236PMCID PMC5338233
• 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.

• Conformational Dynamics of Escherichia coli Flavodoxins in Apo- and Holo-States by Solution NMR Spectroscopy

  2014cited by this paper
• NMR contributions to structural dynamics studies of intrinsically disordered proteins☆

  2014cited by this paper
• Compensatory adaptations of structural dynamics in an intrinsically disordered protein complex.

  2014influential reference
• Protein contact networks: an emerging paradigm in chemistry.

  2013cited by this paper
• Signaling through dynamic linkers as revealed by PKA

  2013cited by this paper
• Protonation‐dependent conformational variability of intrinsically disordered proteins

  2013cited by this paper
• Describing intrinsically disordered proteins at atomic resolution by NMR.

  2013cited by this paper
• Cooperative Unfolding of Compact Conformations of the Intrinsically Disordered Protein Osteopontin

  2013cited by this paper
• 1H, 13C, and 15N backbone and side chain resonance assignments of the C-terminal DNA binding and dimerization domain of v-Myc

  2012cited by this paper
• Overview of metrics and their correlation patterns for multiple-metric topology analysis on heterogeneous graph ensembles.

  2012cited by this paper
• Fuzzy complexes: a more stochastic view of protein function.

  2012cited by this paper
• Mapping allostery through the covariance analysis of NMR chemical shifts

  2011cited by this paper
• Applications of graph theory in protein structure identification

  2011cited by this paper
• Analyzing and visualizing residue networks of protein structures.

  2011cited by this paper
• Prediction of DNA-binding protein based on statistical and geometric features and support vector machines

  2011cited by this paper
• Constructing ensembles for intrinsically disordered proteins.

  2011cited by this paper
• Using graph theory to analyze biological networks

  2011cited by this paper
• The metastasis-associated extracellular matrix protein osteopontin forms transient structure in ligand interaction sites.

  2011cited by this paper
• Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review.

  2011cited by this paper
• Role of the metastasis-promoting protein osteopontin in the tumour microenvironment

  2010cited by this paper
• Intrinsically disordered PEP-19 confers unique dynamic properties to apo and calcium calmodulin.

  2010cited by this paper
• Complex brain networks: graph theoretical analysis of structural and functional systems

  2009cited by this paper
• Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.

  2009cited by this paper
• Assessing the relevance of node features for network structure

  2008cited by this paper
• Probing invisible, low-populated States of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding.

  2008cited by this paper
• Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH

  2008cited by this paper
• Faculty Opinions recommendation of Principal component analysis of the pH-dependent conformational transitions of bovine beta-lactoglobulin monitored by heteronuclear NMR.

  2007cited by this paper
• BioMagResBank

  2007influential reference
• Principal component analysis of the pH-dependent conformational transitions of bovine β-lactoglobulin monitored by heteronuclear NMR

  2007cited by this paper
• The Role of Osteopontin in Tumor Progression and Metastasis in Breast Cancer

  2007cited by this paper
• Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity

  2007cited by this paper
• Handbook of graph theory

  2007cited by this paper
• Fundamentals of Protein NMR Spectroscopy

  2005cited by this paper
• Nerve ending "signal" proteins GAP-43, MARCKS, and BASP1.

  2005cited by this paper
• The role of Osteopontin in tumor metastasis.

  2004cited by this paper
• Structure, function, and dynamics of the dimerization and DNA-binding domain of oncogenic transcription factor v-Myc.

  2001cited by this paper
• Protein flexibility predictions using graph theory

  2001cited by this paper
• Slow dynamics in folded and unfolded states of an SH3 domain.

  2001cited by this paper
• Tikhonov regularization and the L-curve for large discrete ill-posed problems

  2000cited by this paper
• Characterization of collective and anisotropic reorientational protein dynamics.

  2000cited by this paper
• Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: Application to the lac repressor headpiece

  1995cited by this paper
• Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: identification of a binding epitope for DNA.

  1994cited by this paper
• Solution structure of a calmodulin-target peptide complex by multidimensional NMR.

  1994cited by this paper
• Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.

  1983cited by this paper

• Free energy perturbations in enzyme kinetic models reveal cryptic epistasis

  2025cites this paper
• Leveraging network pharmacology for drug discovery: Integrative approaches and emerging insights

  2025cites this paper
• The immune duality of osteopontin and its therapeutic implications for kidney transplantation

  2025cites this paper
• Prediction of influential proteins and enzymes of certain diseases using a directed unimodular hypergraph.

  2024cites this paper
• Pervasive epistasis exposes intramolecular networks in adaptive enzyme evolution

  2023cites this paper
• Higher-order epistasis creates idiosyncrasy, confounding predictions in protein evolution

  2022cites this paper
• Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation.

  2021cites this paper
• Protein conformational switch discerned via network centrality properties

  2021cites this paper
• Biological network analysis with deep learning

  2020cites this paper
• Chokepoints in Mechanical Coupling Associated with Allosteric Proteins: The Pyruvate Kinase Example.

  2019cites this paper
• Molecular Dynamics Simulations of Kir2.2 Interactions with an Ensemble of Cholesterol Molecules.

  2018cites this paper
• Understanding the Structure and Dynamics of Peptides and Proteins Through the Lens of Network Science

  2018cites this paper
• Untersuchung von intrinsisch unstrukturierten Proteinen mithilfe des Austausches mit hyperpolarisiertem Wasser

  2017cites this paper
• NMR probing and visualization of correlated structural fluctuations in intrinsically disordered proteins.

  2017cites this paper
• Investigation of Intrinsically Disordered Proteins through Exchange with Hyperpolarized Water.

  2017cites this paper
• DISSERTATION / DOCTORAL THESIS

  2015cites this paper