Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement (Q36458149)

14 August 2017

Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement (English)

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14 August 2017

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Ning Yu

1

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14 August 2017

Xue Li

2

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14 August 2017

Guanglei Cui

3

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14 August 2017

Seth A Hayik

4

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14 August 2017

Kenneth M Merz

5

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14 August 2017

1 December 2006

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14 August 2017

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14 August 2017

15

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14 August 2017

12

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14 August 2017

2773-2784

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Free R value: a novel statistical quantity for assessing the accuracy of crystal structures

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Crystallographic R factor refinement by molecular dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Force fields for protein simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

The Refined Crystal Structure of an Eel Pout Type III Antifreeze Protein RD1 at 0.62-Å Resolution Reveals Structural Microheterogeneity of Protein and Solvation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Quantum chemical geometry optimizations in proteins using crystallographic raw data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Molecular dynamics applied to X-ray structure refinement

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

An improved hydrogen bond potential: impact on medium resolution protein structures.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Quantum mechanics simulation of protein dynamics on long timescale.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Direct calculation of electron density in density-functional theory

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Refinement of the influenza virus hemagglutinin by simulated annealing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Slow-cooling protocols for crystallographic refinement by simulated annealing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Improved methods for building protein models in electron density maps and the location of errors in these models

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Assigning the protonation states of the key aspartates in β-Secretase using QM/MM X-ray structure refinement

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Impact of a Poisson-Boltzmann electrostatic restraint on protein structures refined at medium resolution.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Protonation status of metal-bound ligands can be determined by quantum refinement

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Time-averaging crystallographic refinement: possibilities and limitations using alpha-cyclodextrin as a test system.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Quantum chemistry can locally improve protein crystal structures.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

An automatic method to generate force-field parameters for hetero-compounds.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242432

Theory and applications of the generalized Born solvation model in macromolecular simulations

21 September 2018

1 reference

12 December 2020

Promise of advances in simulation methods for protein crystallography: implicit solvent models, time-averaging refinement, and quantum mechanical modeling

1 reference

12 December 2020

Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study

1 reference

12 December 2020

Stereochemically restrained refinement of macromolecular structures

1 reference

12 December 2020

Identifiers

DOI

10.1110/PS.062343206

1 reference

14 August 2017

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14 August 2017

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