(Q28479010)

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

SwissParam: A fast force field generation tool for small organic molecules

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Effects of macromolecular crowding on protein conformational changes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Many local motions cooperate to produce the adenylate kinase conformational transition

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

CHARMM: the biomolecular simulation program

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Intrinsic motions along an enzymatic reaction trajectory

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Conformational transitions of adenylate kinase: switching by cracking

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Multiple sequence alignment with the Clustal series of programs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Challenges in enzyme mechanism and energetics

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Stability, Activity and Structure of Adenylate Kinase Mutants

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

The role of dynamic conformational ensembles in biomolecular recognition

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Mesophilic and hyperthermophilic adenylate kinases differ in their tolerance to random fragmentation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Overlap between folding and functional energy landscapes for adenylate kinase conformational change

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Experimental evolution of adenylate kinase reveals contrasting strategies toward protein thermostability

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Global dynamics of proteins: bridging between structure and function

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Functional versus folding landscapes: the same yet different

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Enzyme millisecond conformational dynamics do not catalyze the chemical step

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Insights from coarse-grained Gō models for protein folding and dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Noncooperative folding of subdomains in adenylate kinase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Allosteric regulation and catalysis emerge via a common route.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Bioinformatic method for protein thermal stabilization by structural entropy optimization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Allostery and cooperativity revisited

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Binding-induced folding of a natively unstructured transcription factor.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Protein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Activation mechanism of a signaling protein at atomic resolution from advanced computations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

The mechanism of rate-limiting motions in enzyme function.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

An NMR perspective on enzyme dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Roles of static and dynamic domains in stability and catalysis of adenylate kinase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Reaction coordinates and rates from transition paths

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Protein topology determines binding mechanism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

The role of dynamics in allosteric regulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

The origins of asymmetry in the folding transition states of protein L and protein G.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Theory of protein folding: the energy landscape perspective

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Proteins under extreme physical conditions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

How well can we understand large-scale protein motions using normal modes of elastic network models?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Conservation of mus-ms enzyme motions in the apo- and substrate-mimicked state

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136430

Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

Adjustment of conformational flexibility of glyceraldehyde-3-phosphate dehydrogenase as a means of thermal adaptation and allosteric regulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

Evidence for increased local flexibility in psychrophilic alcohol dehydrogenase relative to its thermophilic homologue

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

Activity and stability of a thermostable alpha-amylase compared to its mesophilic homologue: mechanisms of thermal adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

From transition paths to transition states and rate coefficients.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

Relationship between local structural entropy and protein thermostability

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

Induced-fit movements in adenylate kinases

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002103

Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21779157

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1002103

0 references

DBLP publication ID

journals/ploscb/DailyPC11

1 reference

DBLP Dataset 2021-01-02