Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

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:1854217

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
DOE - Office Of Science; NIGMS
OSTI ID:
1854217
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 journal February 2009
The role of molecular modelling in biomedical research journal April 2006
Advances in protein structure prediction and design journal August 2019
Using quantum chemistry to estimate chemical shifts in biomolecules journal December 2020
Accurate protein structure modeling using sparse NMR data and homologous structure information journal June 2012
Structure of the T4 baseplate and its function in triggering sheath contraction journal May 2016
Modelling structures in cryo-EM maps journal October 2019
Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results journal August 2019
Applying and improving AlphaFold at CASP14 journal November 2021
High‐accuracy protein structure prediction in CASP14 journal July 2021
Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14) journal July 2021
Critical assessment of methods of protein structure prediction (CASP)—Round XIV journal October 2021
Epsin and Sla2 form assemblies through phospholipid interfaces journal January 2018
Assessing the utility of CASP14 models for molecular replacement journal August 2021
Lipid-like Peptides can Stabilize Integral Membrane Proteins for Biophysical and Structural Studies journal July 2017
Features and development of Coot journal March 2010
REFMAC 5 for the refinement of macromolecular crystal structures journal March 2011
The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases journal August 2016
Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases journal March 2017
Multisubunit RNA Polymerases of Jumbo Bacteriophages journal September 2020
Development of Giant Bacteriophage  KZ Is Independent of the Host Transcription Apparatus journal June 2014
Bacterial RNA Polymerase-DNA Interaction—The Driving Force of Gene Expression and the Target for Drug Action journal November 2016
A non-canonical multisubunit RNA polymerase encoded by the AR9 phage recognizes the template strand of its uracil-containing promoters journal April 2017
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination journal February 2017
The arrangement of α-chymotrypsin molecules in the monoclinic crystal form journal January 1964
Recent developments in classical density modification journal March 2010
Phaser crystallographic software journal July 2007
Resolution of phase ambiguity in macromolecular crystallography book January 1985
Determination of macromolecular structures from anomalous diffraction of synchrotron radiation journal October 1991
Using SAD data in Phaser journal March 2011
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core journal July 2018
Structural basis for transcription initiation by bacterial ECF σ factors journal March 2019
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Crystal Structure of ORF210 from E. coli O157:H1 Phage CBA120 (TSP1), a Putative Tailspike Protein journal March 2014
Structure and tailspike glycosidase machinery of ORF212 from E. coli O157:H7 phage CBA120 (TSP3) journal May 2019
Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7 journal September 2020
Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120 journal September 2019
A suggested new bacteriophage genus: “Viunalikevirus” journal June 2012
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard journal December 2007
STAC—A New Domain Associated with Transmembrane Solute Transport and Two-Component Signal Transduction Systems journal October 2015
Some of the most interesting CASP11 targets through the eyes of their authors: CASP11 Target Highlights journal November 2015
The Mechanisms of HAMP-Mediated Signaling in Transmembrane Receptors journal March 2011
The HAMP Domain Structure Implies Helix Rotation in Transmembrane Signaling journal September 2006
Crystallographic snapshot of the Escherichia coli EnvZ histidine kinase in an active conformation journal June 2014
Mechanism of Regulation of Receptor Histidine Kinases journal January 2012
A soluble mutant of the transmembrane receptor Af1503 features strong changes in coiled-coil periodicity journal June 2014
Molecular replacement with MOLREP journal December 2009
Sialidases from gut bacteria: a mini-review journal February 2016
Host sialoglycans and bacterial sialidases: a mucosal perspective journal April 2012
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics journal January 2009
The carbohydrate-active enzymes database (CAZy) in 2013 journal November 2013
Structural Insights into the Catalytic Mechanism of Trypanosoma cruzi trans-Sialidase journal May 2004
Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates journal September 2019
I-TASSER: a unified platform for automated protein structure and function prediction journal March 2010
The I-TASSER Suite: protein structure and function prediction journal December 2014
I-TASSER server for protein 3D structure prediction journal January 2008
The Phyre2 web portal for protein modeling, prediction and analysis journal May 2015
Integrated, rational molecular replacement journal February 2021
Critical assessment of methods of protein structure prediction (CASP)-Round XII journal December 2017
Critical assessment of methods of protein structure prediction (CASP)—Round XIII journal August 2019