A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations (Q37399880)

20 August 2017

A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations (English)

1 reference

20 August 2017

0 references

computational biology

1 reference

1 reference

4

Ivet Bahar

0 references

Angela Gronenborn

object named as

Angela M Gronenborn

series ordinal

3

0 references

Leonardus M I Koharudin

series ordinal

2

object named as

Leonardus M I Koharudin

1 reference

20 August 2017

Lin Liu

1

1 reference

PMC publication ID

2767477

20 August 2017

language of work or name

English

0 references

publication date

1 December 2009

1 reference

20 August 2017

1 reference

20 August 2017

77

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20 August 2017

4

1 reference

20 August 2017

927-939

1 reference

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

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Structure-based protein NMR assignments using native structural ensembles.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Ensemble Refinement of Protein Crystal Structures: Validation and Application

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Protein structural variation in computational models and crystallographic data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Relation between native ensembles and experimental structures of proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Scalable molecular dynamics with NAMD

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Coarse-grained normal mode analysis in structural biology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Simultaneous determination of protein structure and dynamics.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Protein substructures and folded stability

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

PHENIX: building new software for automated crystallographic structure determination

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Molecular dynamics simulations of biomolecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Dynamics of proteins in crystals: comparison of experiment with simple models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

6 September 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Solution structure of cyanovirin-N, a potent HIV-inactivating protein

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

New methods of structure refinement for macromolecular structure determination by NMR.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

MOLMOL: a program for display and analysis of macromolecular structures

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Comparative protein modelling by satisfaction of spatial restraints

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Essential dynamics of proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Conformational substates in a protein: structure and dynamics of metmyoglobin at 80 K.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

The Energy Landscapes and Motions of Proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Conformational substates in proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

vGNM: a better model for understanding the dynamics of proteins in crystals

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Structural flexibility in proteins: impact of the crystal environment.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Analysis of domain motions by approximate normal mode calculations.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2767477

Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy

3 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19688820

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Functional modes of proteins are among the most robust

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19688820

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Study of protein dynamics by X-ray diffraction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19688820

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.22518

1 reference

20 August 2017

1 reference

PMC publication ID

2767477

20 August 2017

PubMed publication ID

19688820

1 reference

PMC publication ID

2767477