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References from Biophysical and computational methods to analyze amino acid interaction networks in proteins. Local targets link to admitted publications; unresolved targets remain external evidence.
Energetics of interactions of regular structural elements in proteins
10.1021/ar00173a003 · 1990 · External reference
Role of loop–helix interactions in stabilizing four-helix bundle proteins
10.1073/pnas.89.16.7315 · 1992 · External reference
10.1080/07391102.2014.984333
10.1080/07391102.2014.984333 · External reference
Modeling proteins as residue interaction networks
10.2174/0929866522666150728115552 · 2015 · External reference
Protein structure and function: looking through the network of side-chain interactions
10.2174/1389203716666150923105727 · 2016 · External reference
Protein contact network topology: a natural language for allostery
10.1016/j.sbi.2015.03.001 · 2015 · External reference
10.1073/pnas.1120536109
10.1073/pnas.1120536109 · External reference
10.1016/j.jmb.2008.06.040
10.1016/j.jmb.2008.06.040 · External reference
10.1016/j.jmb.2008.12.032
10.1016/j.jmb.2008.12.032 · External reference
10.1016/j.cell.2009.07.038
10.1016/j.cell.2009.07.038 · External reference
10.1073/pnas.1218414109
10.1073/pnas.1218414109 · External reference
10.1016/j.sbi.2014.02.004
10.1016/j.sbi.2014.02.004 · External reference
Comparing the intrinsic dynamics of multiple protein structures using elastic network models
10.1016/j.bbagen.2014.09.021 · 2015 · External reference
10.1371/journal.pcbi.1004620
10.1371/journal.pcbi.1004620 · External reference
A critical evaluation of correlated mutation algorithms and coevolution within allosteric mechanisms
10.1007/978-1-61779-334-9_21 · 2012 · External reference
10.1146/annurev-biophys-050511-102305
10.1146/annurev-biophys-050511-102305 · External reference
Construction and analysis of protein–protein interaction networks
10.1186/1759-4499-2-2 · 2010 · External reference
10.1016/j.cell.2011.02.016
10.1016/j.cell.2011.02.016 · External reference
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
10.1107/s0907444904026460 · 2004 · External reference
Recursive domains in proteins
10.1110/ps.24701 · 2002 · External reference
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
10.1038/nsb881 · 2003 · External reference
Graphical rules for enzyme-catalysed rate laws
10.1042/bj1870829 · 1980 · External reference
An extension of Chou's graphic rules for deriving enzyme kinetic equations to systems involving parallel reaction pathways
10.1042/bj2220169 · 1984 · External reference
Graphic rules in steady and non-steady state enzyme kinetics
10.1016/s0021-9258(18)80175-2 · 1989 · External reference
10.1016/s0021-9258(18)82414-0
10.1016/s0021-9258(18)82414-0 · External reference
Kinetics of processive nucleic acid polymerases and nucleases
10.1006/abio.1994.1405 · 1994 · External reference
Applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady-state systems
10.1016/0301-4622(90)80056-d · 1990 · External reference
Graphic rule for drug metabolism systems
10.2174/138920010791514261 · 2010 · External reference
10.1073/pnas.0810961106
10.1073/pnas.0810961106 · External reference
10.1371/journal.pone.0051676
10.1371/journal.pone.0051676 · External reference
10.1073/pnas.1017311108
10.1073/pnas.1017311108 · External reference
Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs
10.1186/1471-2105-12-195 · 2011 · External reference
Exploration of the relationship between topology and designability of conformations
10.1063/1.3596947 · 2011 · External reference
Automated analysis of interatomic contacts in proteins
10.1093/bioinformatics/15.4.327 · 1999 · External reference
10.1021/ci300213c
10.1021/ci300213c · External reference
10.1002/pro.2333
10.1002/pro.2333 · External reference
10.1038/nprot.2012.004
10.1038/nprot.2012.004 · External reference
10.1142/s0219633602000117
10.1142/s0219633602000117 · External reference
10.1016/0022-2836(91)90738-r
10.1016/0022-2836(91)90738-r · External reference
10.1016/j.jmb.2004.10.055
10.1016/j.jmb.2004.10.055 · External reference
10.1103/physreve.64.026118
10.1103/physreve.64.026118 · External reference
10.1021/bi8007559
10.1021/bi8007559 · External reference
Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein's structural organization
10.1186/1471-2105-13-142 · 2012 · External reference
The centrality of a graph
10.1007/bf02289527 · 1966 · External reference
Set of measures of centrality based on betweenness
10.2307/3033543 · 1977 · External reference
10.1021/cr3002356
10.1021/cr3002356 · External reference
10.1093/bioinformatics/bti167
10.1093/bioinformatics/bti167 · External reference
Weighted protein residue networks based on joint recurrences between residues
10.1186/s12859-015-0621-1 · 2015 · External reference
A novel topological centrality measure capturing biologically important proteins
10.1039/c5mb00732a · 2016 · External reference
10.1021/bi200306u
10.1021/bi200306u · External reference
10.1002/prot.24451
10.1002/prot.24451 · External reference
10.1371/journal.pcbi.1003679
10.1371/journal.pcbi.1003679 · External reference
10.1073/pnas.1523573113
10.1073/pnas.1523573113 · External reference
10.1126/science.1130258
10.1126/science.1130258 · External reference
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models
10.1107/s0907444907009791 · 2007 · External reference
10.1107/s0907444909030613
10.1107/s0907444909030613 · External reference
10.1073/pnas.1111325108
10.1073/pnas.1111325108 · External reference
10.1038/nmeth.2592
10.1038/nmeth.2592 · External reference
10.1038/nature08615
10.1038/nature08615 · External reference
10.1016/j.jmb.2015.11.028
10.1016/j.jmb.2015.11.028 · External reference
Biological functions of low-frequency phonons
1977 · External reference
10.1126/science.1749933
10.1126/science.1749933 · External reference
Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA
10.1016/s0006-3495(89)82676-1 · 1989 · External reference
10.1016/0079-6107(92)90023-y
10.1016/0079-6107(92)90023-y · External reference
Low-frequency collective motion in biomacromolecules and its biological functions
10.1016/0301-4622(88)85002-6 · 1988 · External reference
10.1093/protein/gzp012
10.1093/protein/gzp012 · External reference
Low-frequency resonance and cooperativity of hemoglobin
10.1016/0968-0004(89)90026-1 · 1989 · External reference
The biological functions of low-frequency phonons 2. Cooperative effects
1981 · External reference
10.1002/bip.360340114
10.1002/bip.360340114 · External reference
Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
10.1002/prot.340110305 · 1991 · External reference
10.1016/j.jmb.2011.04.078
10.1016/j.jmb.2011.04.078 · External reference
10.1074/jbc.m503444200
10.1074/jbc.m503444200 · External reference
10.1016/j.jmb.2005.05.043
10.1016/j.jmb.2005.05.043 · External reference
10.1002/prot.21146
10.1002/prot.21146 · External reference
Identifying key residues for protein allostery through rigid residue scan
2014 · External reference
10.1371/journal.pcbi.1004542
10.1371/journal.pcbi.1004542 · External reference
Bridging between normal mode analysis and elastic network models
2014 · External reference
10.1002/prot.22875
10.1002/prot.22875 · External reference
The anisotropic network model web server at 2015 (ANM 2.0)
10.1093/bioinformatics/btu847 · 2015 · External reference
10.1016/s1359-0278(97)00024-2
10.1016/s1359-0278(97)00024-2 · External reference
10.1016/s0006-3495(01)76033-x
10.1016/s0006-3495(01)76033-x · External reference
Robust elastic network model: a general modeling for precise understanding of protein dynamics
10.1016/j.jsb.2015.04.007 · 2015 · External reference
Heterogeneous elastic network model improves description of slow motions of proteins in solution
10.1016/j.cplett.2014.11.006 · 2015 · External reference
Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model
2015 · External reference
Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model
10.1186/1472-6807-9-45 · 2009 · External reference
10.1016/j.jmr.2014.01.008
10.1016/j.jmr.2014.01.008 · External reference
Dynamic coupling and allosteric behavior in a nonallosteric protein
10.1021/bi060652l · 2006 · External reference
10.1016/j.jmb.2006.08.076
10.1016/j.jmb.2006.08.076 · External reference
10.1038/srep07306
10.1038/srep07306 · External reference
10.1039/c4cp00110a
10.1039/c4cp00110a · External reference
10.1371/journal.pone.0074347
10.1371/journal.pone.0074347 · External reference
10.1002/pro.2598
10.1002/pro.2598 · External reference
Amino acid networks in a (beta/alpha)(8) barrel enzyme change during catalytic turnover
10.1021/ja501602t · 2014 · External reference
Cryo-crystallography of a true substrate, indole-3-glycerol phosphate, bound to a mutant (alphaD60N) tryptophan synthase alpha2beta2 complex reveals the correct orientation of active site alphaGlu49
10.1074/jbc.273.15.8553 · 1998 · External reference
10.1126/science.286.5438.295
10.1126/science.286.5438.295 · External reference
Covariation of residues in the homeodomain sequence family
10.1002/pro.5560041104 · 1995 · External reference
10.1016/0022-2836(71)90390-1
10.1016/0022-2836(71)90390-1 · External reference
10.1002/prot.10180
10.1002/prot.10180 · External reference
Evolutionarily conserved pathways of energetic connectivity in protein families
1999 · External reference
10.1016/j.jsb.2009.10.009
10.1016/j.jsb.2009.10.009 · External reference
10.1002/prot.22412
10.1002/prot.22412 · External reference
10.1038/nsb881
10.1038/nsb881 · External reference
10.1016/j.cell.2011.10.049
10.1016/j.cell.2011.10.049 · External reference
10.1002/prot.20232
10.1002/prot.20232 · External reference
10.1021/cr100042n
10.1021/cr100042n · External reference
Dynamical network of HIV-1 protease mutants reveals the mechanism of drug resistance and unhindered activity
10.1021/acs.biochem.5b00946 · 2016 · External reference
Allosteric sites: remote control in regulation of protein activity
10.1016/j.sbi.2015.10.004 · 2015 · External reference
10.1016/j.tips.2011.08.004
10.1016/j.tips.2011.08.004 · External reference
10.1021/ar5003158
10.1021/ar5003158 · External reference
10.1021/ar500452q
10.1021/ar500452q · External reference
Solution NMR and computational methods for understanding protein allostery
10.1021/jp312576v · 2013 · External reference
