(Q33696094)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20197040%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

title

Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20197040%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20197040%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

author name string

Bojan Zagrovic

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20197040%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

language of work or name

English

0 references

publication date

1 March 2010

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20197040%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20197040%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

volume

98

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20197040%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20197040%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

page(s)

861-871

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20197040%20AND%20SRC:MED&resulttype=core&format=json

The roles of entropy and kinetics in structure prediction

19 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

All-atom contact model for understanding protein dynamics from crystallographic B-factors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Knowledge-guided laboratory evolution of protein thermolability

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

The High-Resolution NMR Structure of the Early Folding Intermediate of the Thermus thermophilus Ribonuclease H

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

The solution structure and dynamics of human pancreatic ribonuclease determined by NMR spectroscopy provide insight into its remarkable biological activities and inhibition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Progress and challenges in protein structure prediction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

The war of tools: how can NMR spectroscopists detect errors in their structures?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Molecular simulation as an aid to experimentalists.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

On the relationship between the protein structure and protein dynamics.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

On the application of molecular-dynamics simulations to validate thermal parameters and to optimize TLS-group selection for macromolecular refinement.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

NMR: prediction of protein flexibility

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Dynamics of the trimeric AcrB transporter protein inferred from a B-factor analysis of the crystal structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Progress in modeling of protein structures and interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Comment on "Using quaternions to calculate RMSD" [J. Comp. Chem. 25, 1849 (2004)]

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Distributions in protein conformation space: implications for structure prediction and entropy.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

SPICKER: a clustering approach to identify near-native protein folds

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Modeling the Binding Sites of Anti-Hen Egg White Lysozyme Antibodies HyHEL-8 and HyHEL-26: An Insight into the Molecular Basis of Antibody Cross-Reactivity and Specificity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Native-like mean structure in the unfolded ensemble of small proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Flexibility and packing in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Predicting properties of intrinsically unstructured proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Solution structure and dynamics of ribonuclease Sa

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Clustering of low-energy conformations near the native structures of small proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Protein-protein crystal-packing contacts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

NMR structure of the 35-residue villin headpiece subdomain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

VMD: visual molecular dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Comparison of the dynamics of myoglobin in different crystal forms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Rigid protein motion as a model for crystallographic temperature factors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Temperature-dependent X-ray diffraction as a probe of protein structural dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

A free-energy approach for all-atom protein simulation

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Multiple structure alignment by optimal RMSD implies that the average structure is a consensus.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Criteria for downhill protein folding: calorimetry, chevron plot, kinetic relaxation, and single-molecule radius of gyration in chain models with subdued degrees of cooperativity.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Barnase thermal titration via molecular dynamics simulations: detection of early denaturation sites.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Analysis of correlated domain motions in IgG light chain reveals possible mechanisms of immunological signal transduction

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

DRESS: a database of REfined solution NMR structures.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Myosin flexibility: structural domains and collective vibrations.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Protein flexibility and intrinsic disorder

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Protein side-chain rearrangement in regions of point mutations

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Conformation spaces of proteins

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Protein thermal stability: insights from atomic displacement parameters (B values).

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Thousands of proteins likely to have long disordered regions.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Reversible peptide folding in solution by molecular dynamics simulation

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Significance of structural changes in proteins: expected errors in refined protein structures

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Application of the random coil index to studying protein flexibility

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

PDB Improvement Starts with Data Deposition

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2830444

Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations

30 October 2018

1 reference

12 December 2020

Assessing the effect of conformational averaging on the measured values of observables

1 reference

12 December 2020

Dynamical transition of myoglobin in a crystal: comparative studies of X-ray crystallography and Mössbauer spectroscopy

1 reference

12 December 2020

Beta-hairpin folding simulations in atomistic detail using an implicit solvent model

1 reference

12 December 2020

Efficient RMSD measures for the comparison of two molecular ensembles. Root-mean-square deviation

1 reference

12 December 2020

Flexibility analysis of enzyme active sites by crystallographic temperature factors

1 reference

12 December 2020

Is one solution good enough?

1 reference

12 December 2020

All-atom ab initio folding of a diverse set of proteins

1 reference

12 December 2020

fRMSDPred: predicting local RMSD between structural fragments using sequence information

1 reference

12 December 2020

Computational Analysis of the Mechanism and Thermodynamics of Inhibition of Phosphodiesterase 5A by Synthetic Ligands

1 reference

12 December 2020

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

1 reference

12 December 2020

Relationship of protein flexibility to thermostability

1 reference

12 December 2020

The radius of gyration of an apomyoglobin folding intermediate

1 reference

12 December 2020

Accuracy of protein flexibility predictions

1 reference

12 December 2020

Correlation between side chain mobility and conformation in protein structures

1 reference

12 December 2020

10.1016/J.BPJ.2009.11.011

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20197040%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20197040%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

PubMed publication ID

20197040

1 reference