Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling (Q33327065)

25 July 2017

title

Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling (English)

1 reference

25 July 2017

6

Eddy Arnold

1 reference

25 July 2017

Jennifer L Knight

1

1 reference

25 July 2017

Zhiyong Zhou

2

1 reference

25 July 2017

Emilio Gallicchio

3

1 reference

25 July 2017

Daniel M Himmel

4

1 reference

25 July 2017

Richard A Friesner

5

1 reference

25 July 2017

Ronald M Levy

7

1 reference

25 July 2017

publication date

19 March 2008

1 reference

Acta Crystallographica Section D: Biological Crystallography

25 July 2017

published in

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25 July 2017

volume

64

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25 July 2017

issue

Pt 4

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25 July 2017

page(s)

383-396

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High-resolution structure prediction and the crystallographic phase problem

25 July 2017

cites work

1 reference

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Crystallographic R factor refinement by molecular dynamics

21 June 2018

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Normal-Mode Refinement of Anisotropic Thermal Parameters for Potassium Channel KcsA at 3.2 Å Crystallographic Resolution

21 June 2018

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

21 June 2018

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Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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Protein structural transitions and their functional role

21 June 2018

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21 June 2018

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Full-matrix refinement of the protein crambin at 0.83 A and 130 K.

21 June 2018

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xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets

21 June 2018

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Anchor residues in protein-protein interactions

21 June 2018

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Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography.

21 June 2018

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A hierarchical approach to all-atom protein loop prediction

21 June 2018

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Exploring the range of protein flexibility, from a structural proteomics perspective

21 June 2018

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Announcing the worldwide Protein Data Bank

21 June 2018

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Role of an N-terminal site of Ubc9 in SUMO-1, -2, and -3 binding and conjugation

21 June 2018

1 reference

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Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction.

21 June 2018

1 reference

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Molecular dynamics applied to X-ray structure refinement

21 June 2018

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Principles of docking: An overview of search algorithms and a guide to scoring functions

21 June 2018

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Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1

21 June 2018

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Synthesis and comparative molecular field analysis (CoMFA) of symmetric and nonsymmetric cyclic sulfamide HIV-1 protease inhibitors

21 June 2018

1 reference

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Use of TLS parameters to model anisotropic displacements in 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=2631124

The 1.0 A crystal structure of Ca(2+)-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2631124

Crystal structure of Escherichia coli CyaY protein reveals a previously unidentified fold for the evolutionarily conserved frataxin family

21 June 2018

1 reference

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Validation of protein crystal structures

21 June 2018

1 reference

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The binding interface between an E2 (UBC9) and a ubiquitin homologue (UBL1).

21 June 2018

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Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography

21 June 2018

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

21 June 2018

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Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system

21 June 2018

1 reference

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Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution

21 June 2018

1 reference

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Structure-based design of symmetric inhibitors of HIV-1 protease.

21 June 2018

1 reference

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Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution

21 June 2018

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Refinement of protein dynamic structure: normal mode refinement

21 June 2018

1 reference

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How calmodulin binds its targets: sequence independent recognition of amphiphilic alpha-helices

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2631124

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2631124

Long loop prediction using the protein local optimization program.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2631124

Crystallographic refinement by knowledge-based exploration of complex energy landscapes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2631124

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2631124

Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2631124

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2631124

Protein conformational substates from X-ray crystallography

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2631124

The impact of protein flexibility on protein-protein docking

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2631124

Exploration of disorder in protein structures by X-ray restrained molecular dynamics

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2631124

Is one solution good enough?

31 October 2018

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12 December 2020

Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics

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12 December 2020

Annealing in crystallography: a powerful optimization tool

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12 December 2020

CORRELATION OF STRUCTURE AND FUNCTION IN ENZYME ACTION

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12 December 2020

Structural heterogeneity in protein crystals

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12 December 2020

Temperature-dependent molecular dynamics and restrained X-ray refinement simulations of a Z-DNA hexamer

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12 December 2020

Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics

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12 December 2020

Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations

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12 December 2020

Recent developments for the efficient crystallographic refinement of macromolecular structures

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12 December 2020

Conformational flexibility of a ubiquitin conjugation enzyme (E2)

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12 December 2020

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

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12 December 2020

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility

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12 December 2020

On the Role of the Crystal Environment in Determining Protein Side-chain Conformations

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12 December 2020

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

12 December 2020

10.1107/S090744490800070X

Identifiers

DOI

1 reference

release_bznta5j46zexxehfpeltzxjvxi

25 July 2017

Fatcat ID

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Fatcat

https://api.fatcat.wiki/v0/release/bznta5j46zexxehfpeltzxjvxi

24 November 2022

mapped directly with Wikidata item

PMC publication ID

2631124

1 reference

25 July 2017

1 reference