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Computational models in the service of X-ray and cryo-electron microscopy structure determination

Journal Article · · Proteins
DOI:https://doi.org/10.1002/prot.26223· OSTI ID:1856413

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
DOE - Office Of Science; NIGMS
OSTI ID:
1856413
Journal Information:
Proteins, Vol. 89, Issue (12)
Country of Publication:
United States
Language:
ENGLISH

References (60)

Outcome of a Workshop on Applications of Protein Models in Biomedical Research February 2009
The role of molecular modelling in biomedical research April 2006
Advances in protein structure prediction and design August 2019
Using quantum chemistry to estimate chemical shifts in biomolecules December 2020
Accurate protein structure modeling using sparse NMR data and homologous structure information June 2012
Structure of the T4 baseplate and its function in triggering sheath contraction May 2016
Modelling structures in cryo-EM maps October 2019
Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results August 2019
Applying and improving AlphaFold at CASP14 November 2021
High‐accuracy protein structure prediction in CASP14 July 2021
Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14) July 2021
Critical assessment of methods of protein structure prediction (CASP)—Round XIV October 2021
Epsin and Sla2 form assemblies through phospholipid interfaces January 2018
Assessing the utility of CASP14 models for molecular replacement August 2021
Lipid-like Peptides can Stabilize Integral Membrane Proteins for Biophysical and Structural Studies July 2017
Features and development of Coot March 2010
REFMAC 5 for the refinement of macromolecular crystal structures March 2011
The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases August 2016
Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases March 2017
Multisubunit RNA Polymerases of Jumbo Bacteriophages September 2020
Development of Giant Bacteriophage  KZ Is Independent of the Host Transcription Apparatus June 2014
Bacterial RNA Polymerase-DNA Interaction—The Driving Force of Gene Expression and the Target for Drug Action November 2016
A non-canonical multisubunit RNA polymerase encoded by the AR9 phage recognizes the template strand of its uracil-containing promoters April 2017
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination February 2017
The arrangement of α-chymotrypsin molecules in the monoclinic crystal form January 1964
Recent developments in classical density modification March 2010
Phaser crystallographic software July 2007
Resolution of phase ambiguity in macromolecular crystallography January 1985
Determination of macromolecular structures from anomalous diffraction of synchrotron radiation October 1991
Using SAD data in Phaser March 2011
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core July 2018
Structural basis for transcription initiation by bacterial ECF σ factors March 2019
PHENIX: a comprehensive Python-based system for macromolecular structure solution January 2010
Crystal Structure of ORF210 from E. coli O157:H1 Phage CBA120 (TSP1), a Putative Tailspike Protein March 2014
Structure and tailspike glycosidase machinery of ORF212 from E. coli O157:H7 phage CBA120 (TSP3) May 2019
Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7 September 2020
Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120 September 2019
A suggested new bacteriophage genus: “Viunalikevirus” June 2012
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard December 2007
STAC—A New Domain Associated with Transmembrane Solute Transport and Two-Component Signal Transduction Systems October 2015
Some of the most interesting CASP11 targets through the eyes of their authors: CASP11 Target Highlights November 2015
The Mechanisms of HAMP-Mediated Signaling in Transmembrane Receptors March 2011
The HAMP Domain Structure Implies Helix Rotation in Transmembrane Signaling September 2006
Crystallographic snapshot of the Escherichia coli EnvZ histidine kinase in an active conformation June 2014
Mechanism of Regulation of Receptor Histidine Kinases January 2012
A soluble mutant of the transmembrane receptor Af1503 features strong changes in coiled-coil periodicity June 2014
Molecular replacement with MOLREP December 2009
Sialidases from gut bacteria: a mini-review February 2016
Host sialoglycans and bacterial sialidases: a mucosal perspective April 2012
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics January 2009
The carbohydrate-active enzymes database (CAZy) in 2013 November 2013
Structural Insights into the Catalytic Mechanism of Trypanosoma cruzi trans-Sialidase May 2004
Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates September 2019
I-TASSER: a unified platform for automated protein structure and function prediction March 2010
The I-TASSER Suite: protein structure and function prediction December 2014
I-TASSER server for protein 3D structure prediction January 2008
The Phyre2 web portal for protein modeling, prediction and analysis May 2015
Integrated, rational molecular replacement February 2021
Critical assessment of methods of protein structure prediction (CASP)-Round XII December 2017
Critical assessment of methods of protein structure prediction (CASP)—Round XIII August 2019