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Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/prot.20226openalex-snapshot
Escherichia coli adenylate kinase dynamics: Comparison of elastic network model modes with mode‐coupling 15N‐NMR relaxation data
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Activation of Adenylate Kinase by Denaturants Is Due to the Increasing Conformational Flexibility at Its Active Sites
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Domain Closure in Adenylate Kinase
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Comment on a “Fluctuation and Cross Correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations”
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Identifying the protein folding nucleus using molecular dynamics
inferredcites →https://doi.org/10.1007/s00018-005-5236-7openalex-snapshot
Protein flexibility: its role in structure and mechanism revealed by molecular simulations
inferredcites →https://doi.org/10.1016/j.chembiol.2004.06.007openalex-snapshot
Protein Motions Promote Catalysis
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Progress in computational protein design
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A new type of metal-binding site in cobalt- and zinc-containing adenylate kinases isolated from sulfate-reducers Desulfovibrio gigas and Desulfovibrio desulfuricans ATCC 27774
inferredcites →https://doi.org/10.1016/j.jmb.2005.07.031openalex-snapshot
Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model: Adenylate Kinase
inferredcites →https://doi.org/10.1016/j.jmb.2006.11.085openalex-snapshot
Conformational Transitions of Adenylate Kinase: Switching by Cracking
inferredcites →https://doi.org/10.1016/j.jmb.2007.08.047openalex-snapshot
Allosteric Communication in Dihydrofolate Reductase: Signaling Network and Pathways for Closed to Occluded Transition and Back
inferredcites →https://doi.org/10.1016/j.jsb.2008.09.003openalex-snapshot
Coevolving residues of (β/α)8-barrel proteins play roles in stabilizing active site architecture and coordinating protein dynamics
inferredcites →https://doi.org/10.1016/j.progpolymsci.2005.01.012openalex-snapshot
The role of dynamically correlated conformational equilibria in the folding of macromolecular structures. A model for the design of folded dendrimers
inferredcites →https://doi.org/10.1016/j.sbi.2006.06.013openalex-snapshot
Knowledge-based potentials in protein design
inferredcites →https://doi.org/10.1016/s0968-0004(00)89105-7openalex-snapshot
Dali: a network tool for protein structure comparison
inferredcites →https://doi.org/10.1016/s0968-0004(01)01811-4openalex-snapshot
Cooperative hemoglobins: conserved fold, diverse quaternary assemblies and allosteric mechanisms
inferredcites →https://doi.org/10.1016/s0969-2126(96)00018-4openalex-snapshot
Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding
inferredcites →https://doi.org/10.1021/bi00188a001openalex-snapshot
Structural Mechanisms for Domain Movements in Proteins
inferredcites →https://doi.org/10.1021/ja0514949openalex-snapshot
Conservation of μs−ms Enzyme Motions in the Apo- and Substrate-Mimicked State
inferredcites →https://doi.org/10.1021/ja075055gopenalex-snapshot
NMR Identification of Transient Complexes Critical to Adenylate Kinase Catalysis
inferredcites →https://doi.org/10.1021/ja803928mopenalex-snapshot
Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole
inferredcites →https://doi.org/10.1038/nature03990openalex-snapshot
Natural-like function in artificial WW domains
inferredcites →https://doi.org/10.1038/nature03991openalex-snapshot
Evolutionary information for specifying a protein fold
inferredcites →https://doi.org/10.1038/nature04105openalex-snapshot
Intrinsic dynamics of an enzyme underlies catalysis
inferredcites →https://doi.org/10.1038/nature06407openalex-snapshot
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
inferredcites →https://doi.org/10.1038/nature06410openalex-snapshot
Intrinsic motions along an enzymatic reaction trajectory
inferredcites →https://doi.org/10.1038/nature06522openalex-snapshot
Dynamic personalities of proteins
inferredcites →https://doi.org/10.1038/nchembio.98openalex-snapshot
Allosteric regulation and catalysis emerge via a common route
inferredcites →https://doi.org/10.1038/nchembio0108-21openalex-snapshot
What determines the speed limit on enzyme catalysis?
inferredcites →https://doi.org/10.1038/nsb881openalex-snapshot
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
inferredcites →https://doi.org/10.1038/nsb991openalex-snapshot
Covariation of backbone motion throughout a small protein domain
inferredcites →https://doi.org/10.1038/nsmb821openalex-snapshot
Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair
inferredcites →https://doi.org/10.1063/1.2973624openalex-snapshot
Identifying critical residues in protein folding: Insights from ϕ-value and Pfold analysis
inferredcites →https://doi.org/10.1073/pnas.0405502101openalex-snapshot
Anticorrelated motions as a driving force in enzyme catalysis: The dehydrogenase reaction
inferredcites →https://doi.org/10.1073/pnas.0408930102openalex-snapshot
Molecular dynamics and protein function
inferredcites →https://doi.org/10.1073/pnas.0409128102openalex-snapshot
Statistical coevolution analysis and molecular dynamics: Identification of amino acid pairs essential for catalysis
inferredcites →https://doi.org/10.1073/pnas.0510426103openalex-snapshot
Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
inferredcites →https://doi.org/10.1073/pnas.0702551104openalex-snapshot
The mechanism of rate-limiting motions in enzyme function
inferredcites →https://doi.org/10.1073/pnas.0906510106openalex-snapshot
Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins
inferredcites →https://doi.org/10.1073/pnas.2135471100openalex-snapshot
Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
inferredcites →https://doi.org/10.1073/pnas.2628068100openalex-snapshot
Watching proteins fold one molecule at a time
inferredcites →https://doi.org/10.1074/jbc.273.30.19097openalex-snapshot
Genetically Engineered Zinc-chelating Adenylate Kinase fromEscherichia coli with Enhanced Thermal Stability
inferredcites →https://doi.org/10.1074/jbc.273.30.19102openalex-snapshot
Structural and Energetic Factors of the Increased Thermal Stability in a Genetically Engineered Escherichia coliAdenylate Kinase
inferredcites →https://doi.org/10.1074/jbc.m707632200openalex-snapshot
Conformational Transitions in Adenylate Kinase
inferredcites →https://doi.org/10.1093/bioinformatics/14.10.892openalex-snapshot
JPred: a consensus secondary structure prediction server.
inferredcites →https://doi.org/10.1093/bioinformatics/19.1.167openalex-snapshot
Detection of hydrogen-bond signature patterns in protein families
inferredcites →https://doi.org/10.1093/bioinformatics/bth431openalex-snapshot
PCOAT: positional correlation analysis using multiple methods
inferredcites →https://doi.org/10.1093/bioinformatics/btl448openalex-snapshot
Anisotropic network model: systematic evaluation and a new web interface
inferredcites →https://doi.org/10.1093/bioinformatics/btm098openalex-snapshot
UniRef: comprehensive and non-redundant UniProt reference clusters
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1107/s0108767304098332openalex-snapshot
CCP4 molecular graphics project
inferredcites →https://doi.org/10.1107/s0907444904023716openalex-snapshot
Developments in theCCP4 molecular-graphics project
inferredcites →https://doi.org/10.1110/ps.073390208openalex-snapshot
Correspondences between low‐energy modes in enzymes: Dynamics‐based alignment of enzymatic functional families
inferredcites →https://doi.org/10.1126/science.1169375openalex-snapshot
Protein Dynamism and Evolvability
inferredcites →https://doi.org/10.1126/science.286.5438.295openalex-snapshot
Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families
inferredcites →https://doi.org/10.1128/jb.101.3.763-769.1970openalex-snapshot
Comparative Allostery of 3-Deoxy- d - Arabino -Heptulosonate-7-Phosphate Synthetase as a Molecular Basis for Classification
inferredcites →https://doi.org/10.1146/annurev.biochem.75.103004.142800openalex-snapshot
Relating Protein Motion to Catalysis
inferredcites →https://doi.org/10.1146/annurev.pharmtox.47.120505.105159openalex-snapshot
Allosteric Modulation of G Protein–Coupled Receptors
inferredcites →https://doi.org/10.1186/1471-2105-5-113openalex-snapshot
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
inferredcites →https://doi.org/10.1186/1472-6807-8-23openalex-snapshot
Exploring allosteric coupling in the α-subunit of Heterotrimeric G proteins using evolutionary and ensemble-based approaches
inferredcites →https://doi.org/10.1186/1475-2859-5-2openalex-snapshot
Enzymes: An integrated view of structure, dynamics and function
inferredcites →https://doi.org/10.1186/1752-153x-2-17openalex-snapshot
Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family
inferredcites →https://doi.org/10.1371/journal.pcbi.1000531openalex-snapshot
Structure-Based Predictive Models for Allosteric Hot Spots
inferredcites →https://doi.org/10.1529/biophysj.107.105270openalex-snapshot
Allosteric Transitions in the Chaperonin GroEL are Captured by a Dominant Normal Mode that is Most Robust to Sequence Variations
inferredcites →https://doi.org/10.1529/biophysj.108.135467openalex-snapshot
Small- and Large-Scale Conformational Changes of Adenylate Kinase: A Molecular Dynamics Study of the Subdomain Motion and Mechanics
inferredcites →https://doi.org/10.2144/03342mt01openalex-snapshot
TM4: A Free, Open-Source System for Microarray Data Management and Analysis
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Normal Mode Dynamics Comparison of Proteins
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Computational Exploration of Conformational Transitions in Protein Drug Targets
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Associating protein sequence positions with the modulation of quantitative phenotypes
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Structural investigation of the cold-adapted acylaminoacyl peptidase from Sporosarcina psychrophila by atomistic simulations and biophysical methods
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Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase
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Identification and structural characterization of deleterious non-synonymous single nucleotide polymorphisms in the human SKP2 gene
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Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms
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Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal α-helix in an acylaminoacyl peptidase
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Mechanical variations in proteins with large-scale motions highlight the formation of structural locks
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Computational approaches to mapping allosteric pathways
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(Dis)similarity Index To Compare Correlated Motions in Molecular Simulations
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xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures.
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PhISCO: a simple method to infer phenotypes from protein sequences
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Hybrid approaches for the detection of networks of critical residues involved in functional motions in protein families
inferred← citeshttps://doi.org/10.1371/journal.pone.0035686openalex-snapshot
Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation
inferred← citeshttps://doi.org/10.2174/1574893611308020003openalex-snapshot
Identifying Coevolution Between Amino Acid Residues in Protein Families: Advances in the Improvement and Evaluation of Correlated Mutation Algorithms
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