StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement

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