Segmented transition pathway of the signaling protein nitrogen regulatory protein C (Q30491157)

3 November 2017

Segmented transition pathway of the signaling protein nitrogen regulatory protein C (English)

1 reference

3 November 2017

5

Martin Karplus

1 reference

3 November 2017

Ming Lei

1

1 reference

3 November 2017

Janice Velos

2

1 reference

3 November 2017

Alexandra Gardino

3

1 reference

3 November 2017

Alexsandr Kivenson

4

1 reference

3 November 2017

Dorothee Kern

6

1 reference

3 November 2017

language of work or name

English

0 references

publication date

1 July 2009

1 reference

Journal of Molecular Biology

3 November 2017

1 reference

3 November 2017

392

1 reference

3 November 2017

3

1 reference

3 November 2017

823-836

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

3 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Allostery and cooperativity revisited

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Recent advances in implicit solvent-based methods for biomolecular simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Finding transition pathways using the string method with swarms of trajectories

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Dynamic personalities of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Intrinsic motions along an enzymatic reaction trajectory

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Mechanism of Na+/H+ antiporting.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Conformational transitions of adenylate kinase: switching by cracking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Evaluating protein structures determined by structural genomics consortia

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

The changing landscape of protein allostery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Out-of-plane motions in open sliding clamps: molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

NMR data collection and analysis protocol for high-throughput protein structure determination

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

The role of dynamics in allosteric regulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Refinement of protein structures in explicit solvent

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Escaping free-energy minima

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Conformational pathways in the gating of Escherichia coli mechanosensitive channel

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Folding and binding cascades: dynamic landscapes and population shifts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Structure of a transiently phosphorylated switch in bacterial signal transduction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Torsion angle dynamics for NMR structure calculation with the new program DYANA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Calculation of pathways for the conformational transition between the GTP- and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

VMD: visual molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Errors in protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Essential dynamics of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Three-dimensional solution structure of the N-terminal receiver domain of NTRC

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Dynamics of proteins: elements and function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

WHAT IF: a molecular modeling and drug design program

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

The Energy Landscapes and Motions of Proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Functional dynamics of response regulators using NMR relaxation techniques.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

A modified TIP3P water potential for simulation with Ewald summation

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

DRESS: a database of REfined solution NMR structures.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2765875

Targeted molecular dynamics: a new approach for searching pathways of conformational transitions

26 November 2018

1 reference

12 December 2020

Pathways for conformational change in nitrogen regulatory protein C from discrete path sampling

1 reference

12 December 2020

Protein structural change upon ligand binding: linear response theory

1 reference

12 December 2020

Molecular dynamic simulations of the N-terminal receiver domain of NtrC reveal intrinsic conformational flexibility in the inactive state

1 reference

12 December 2020

Improving the quality of protein structures derived by NMR spectroscopy

1 reference

12 December 2020

The essential dynamics of thermolysin: Confirmation of the hinge-bending motion and comparison of simulations in vacuum and water

1 reference

12 December 2020

Predicting slow structural transitions in macromolecular systems: Conformational flooding

1 reference

12 December 2020

Two-state allosteric behavior in a single-domain signaling protein

1 reference

12 December 2020

Finite temperature string method for the study of rare events.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2009.06.065

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2009.06.065

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2009.06.065

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2009.06.065

Identifiers

DOI

10.1016/J.JMB.2009.06.065

1 reference

3 November 2017

1 reference

3 November 2017

PubMed publication ID

19576227

1 reference