标题
StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement
作者
关键词
-
出版物
Nature Protocols
Volume -, Issue -, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2022-11-03
DOI
10.1038/s41596-022-00757-9
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Mechanism of AAA+ ATPase-mediated RuvAB–Holliday junction branch migration
- (2022) Jiri Wald et al. NATURE
- The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP
- (2021) Grzegorz Chojnowski et al. Acta Crystallographica Section D-Structural Biology
- Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking
- (2021) Hahnbeom Park et al. Journal of Chemical Theory and Computation
- Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation
- (2021) Sean Miletic et al. Nature Communications
- Structure and dynamics of a mycobacterial type VII secretion system
- (2021) Catalin M. Bunduc et al. NATURE
- Highly accurate protein structure prediction with AlphaFold
- (2021) John Jumper et al. NATURE
- Python‐based Helix Indexer: A graphical user interface program for finding symmetry of helical assembly through Fourier–Bessel indexing of electron microscopic data
- (2021) Xuewu Zhang PROTEIN SCIENCE
- Accurate prediction of protein structures and interactions using a three-track neural network
- (2021) Minkyung Baek et al. SCIENCE
- DeepEMhancer: a deep learning solution for cryo-EM volume post-processing
- (2021) Ruben Sanchez-Garcia et al. Communications Biology
- Structural Dynamics of the Functional Nonameric Type III Translocase Export Gate
- (2021) Biao Yuan et al. JOURNAL OF MOLECULAR BIOLOGY
- AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
- (2021) Mihaly Varadi et al. NUCLEIC ACIDS RESEARCH
- Macromolecular modeling and design in Rosetta: recent methods and frameworks
- (2020) Julia Koehler Leman et al. NATURE METHODS
- Structural basis of CXC chemokine receptor 2 activation and signalling
- (2020) Kaiwen Liu et al. NATURE
- Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination
- (2020) Ryan E. Pavlovicz et al. PLoS Computational Biology
- Density modification of cryo-EM maps
- (2020) Thomas C. Terwilliger et al. Acta Crystallographica Section D-Structural Biology
- cryo_fit: Democratization of Flexible Fitting for Cryo-EM
- (2019) Doo Nam Kim et al. JOURNAL OF STRUCTURAL BIOLOGY
- Fast, efficient fragment-based coordinate generation for Open Babel
- (2019) Naruki Yoshikawa et al. Journal of Cheminformatics
- Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps
- (2019) Rune Thomas Kidmose et al. IUCrJ
- Cryo-EM structure of pleconaril-resistant rhinovirus-B5 complexed to the antiviral OBR-5-340 reveals unexpected binding site
- (2019) Jiri Wald et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Point-group symmetry detection in three-dimensional charge density of biomolecules
- (2019) Cyril F Reboul et al. BIOINFORMATICS
- SWISS-MODEL: homology modelling of protein structures and complexes
- (2018) Andrew Waterhouse et al. NUCLEIC ACIDS RESEARCH
- Cryo-EM structure of the bacterial actin AlfA reveals unique assembly and ATP-binding interactions and the absence of a conserved subdomain
- (2018) Gülsima D. Usluer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps
- (2018) Tristan Ian Croll Acta Crystallographica Section D-Structural Biology
- Real-space refinement in PHENIX for cryo-EM and crystallography
- (2018) Pavel V. Afonine et al. Acta Crystallographica Section D-Structural Biology
- De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes
- (2018) Kalli Kappel et al. NATURE METHODS
- A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps
- (2018) Thomas C. Terwilliger et al. NATURE METHODS
- Automatically Fixing Errors in Glycoprotein Structures with Rosetta
- (2018) Brandon Frenz et al. STRUCTURE
- New tools for automated high-resolution cryo-EM structure determination in RELION-3
- (2018) Jasenko Zivanov et al. eLife
- The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
- (2017) Rebecca F. Alford et al. Journal of Chemical Theory and Computation
- Helical reconstruction in RELION
- (2017) Shaoda He et al. JOURNAL OF STRUCTURAL BIOLOGY
- Structural basis for the initiation of eukaryotic transcription-coupled DNA repair
- (2017) Jun Xu et al. NATURE
- RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps
- (2017) Brandon Frenz et al. NATURE METHODS
- Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states
- (2017) Xiaoyuan Zhou et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM
- (2017) Soung-Hun Roh et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel
- (2017) Zachary M. James et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- UCSF ChimeraX: Meeting modern challenges in visualization and analysis
- (2017) Thomas D. Goddard et al. PROTEIN SCIENCE
- High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective
- (2017) Alexander Wlodawer et al. STRUCTURE
- Structure of human immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits activated lymphocytes
- (2017) Ruda de Luna Almeida Santos et al. Nature Communications
- Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states
- (2017) Xiaoyuan Zhou et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
- (2017) Sheng Wang et al. PLoS Computational Biology
- Ligand fitting with CCP4
- (2017) Robert A. Nicholls Acta Crystallographica Section D-Structural Biology
- AceDRG: a stereochemical description generator for ligands
- (2017) Fei Long et al. Acta Crystallographica Section D-Structural Biology
- De Novo modeling in cryo-EM density maps with Pathwalking
- (2016) Muyuan Chen et al. JOURNAL OF STRUCTURAL BIOLOGY
- Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2)
- (2016) Mariana Grieben et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2)
- (2016) Mariana Grieben et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
- (2016) Ray Yu-Ruei Wang et al. eLife
- Data-collection strategy for challenging native SAD phasing
- (2016) Vincent Olieric et al. Acta Crystallographica Section D-Structural Biology
- Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement
- (2015) Frank DiMaio et al. NATURE METHODS
- The I-TASSER Suite: protein structure and function prediction
- (2015) Jianyi Yang et al. NATURE METHODS
- Activities at the Universal Protein Resource (UniProt)
- (2014) NUCLEIC ACIDS RESEARCH
- The Resolution Revolution
- (2014) W. Kuhlbrandt SCIENCE
- Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
- (2014) Sergey Ovchinnikov et al. eLife
- Crystallization and preliminary crystallographic analysis of human aquaporin 1 at a resolution of 3.28 Å
- (2014) David Ruiz Carrillo et al. Acta Crystallographica Section F-Structural Biology Communications
- Improved low-resolution crystallographic refinement with Phenix and Rosetta
- (2013) Frank DiMaio et al. NATURE METHODS
- Cross-Link Guided Molecular Modeling with ROSETTA
- (2013) Abdullah Kahraman et al. PLoS One
- Problems in obtaining perfect images by single-particle electron cryomicroscopy of biological structures in amorphous ice
- (2013) Richard Henderson et al. Microscopy
- RCrane: semi-automated RNA model building
- (2012) Kevin S. Keating et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Towards automated crystallographic structure refinement withphenix.refine
- (2012) Pavel V. Afonine et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Cryo-electron microscopy - a primer for the non-microscopist
- (2012) Jacqueline L. S. Milne et al. FEBS Journal
- Atomic model of the type III secretion system needle
- (2012) Antoine Loquet et al. NATURE
- Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design
- (2012) P. Douglas Renfrew et al. PLoS One
- RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
- (2011) Sarel J. Fleishman et al. PLoS One
- Protein 3D Structure Computed from Evolutionary Sequence Variation
- (2011) Debora S. Marks et al. PLoS One
- Features and development ofCoot
- (2010) P. Emsley et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
- (2010) F. Jossinet et al. BIOINFORMATICS
- 3.3 Å Cryo-EM Structure of a Nonenveloped Virus Reveals a Priming Mechanism for Cell Entry
- (2010) Xing Zhang et al. CELL
- EMDataBank.org: unified data resource for CryoEM
- (2010) C. L. Lawson et al. NUCLEIC ACIDS RESEARCH
- Averaged kick maps: less noise, more signal…and probably less bias
- (2009) Jure Pražnikar et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta
- (2009) Frank DiMaio et al. JOURNAL OF MOLECULAR BIOLOGY
- A Novel Mirror-symmetry Analysis Approach for the Study of Macromolecular Assemblies Imaged by Electron Microscopy
- (2008) Alessandro Costa et al. JOURNAL OF MOLECULAR BIOLOGY
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreDiscover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversation