findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM

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

Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells

(2021) Dimitry Tegunov et al.   NATURE METHODS

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

(2021) Catherine L. Lawson et al.   NATURE METHODS

Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching

(2021) Thomas C. Terwilliger et al.   Acta Crystallographica Section D-Structural Biology

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Structure of the mycobacterial ESX-5 type VII secretion system pore complex

(2021) Katherine S. H. Beckham et al.   Science Advances

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution

(2020) Grzegorz Chojnowski et al.   Acta Crystallographica Section D-Structural Biology

Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM

(2020) Soon Wen Hoh et al.   Acta Crystallographica Section D-Structural Biology

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes

(2020) Jonas Pfab et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence assignment for low-resolution modelling of protein crystal structures

(2019) Grzegorz Chojnowski et al.   Acta Crystallographica Section D-Structural Biology

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu

(2019) Chi-Min Ho et al.   NATURE METHODS

Using Phaser and ensembles to improve the performance of SIMBAD

(2019) Adam J. Simpkin et al.   Acta Crystallographica Section D-Structural Biology

Molecular mechanisms underlying intraspecific variation in snake venom

(2018) Diana R. Amazonas et al.   Journal of Proteomics

The 3.5-Å CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase V o Proton Channel

(2018) Soung-Hun Roh et al.   MOLECULAR CELL

Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A

(2018) Marcus Fislage et al.   NUCLEIC ACIDS RESEARCH

De novo main-chain modeling for EM maps using MAINMAST

(2018) Genki Terashi et al.   Nature Communications

Automated map sharpening by maximization of detail and connectivity

(2018) Thomas C. Terwilliger et al.   Acta Crystallographica Section D-Structural Biology

SIMBAD: a sequence-independent molecular-replacement pipeline

(2018) Adam J. Simpkin et al.   Acta Crystallographica Section D-Structural Biology

Distributed computing for macromolecular crystallography

(2018) Evgeny Krissinel et al.   Acta Crystallographica Section D-Structural Biology

Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes

(2018) David J. F. Ramrath et al.   SCIENCE

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps

(2018) Thomas C. Terwilliger et al.   NATURE METHODS

Structure determination of contaminant proteins using the MarathonMR procedure

(2017) Kaushik Hatti et al.   JOURNAL OF STRUCTURAL BIOLOGY

Model-based local density sharpening of cryo-EM maps

(2017) Arjen J Jakobi et al.   eLife

Dali server update

(2016) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

Protein purification and crystallization artifacts: The tale usually not told

(2016) Ewa Niedzialkowska et al.   PROTEIN SCIENCE

Neutralization of toxicological activities of medically-relevant Bothrops snake venoms and relevant toxins by two polyvalent bothropic antivenoms produced in Peru and Brazil

(2016) Maria I. Estevao-Costa et al.   TOXICON

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

(2016) Ray Yu-Ruei Wang et al.   eLife

Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations

(2016) Przemyslaw Jerzy Porebski et al.   Acta Crystallographica Section D-Structural Biology

The 1.1 Å resolution structure of a periplasmic phosphate-binding protein fromStenotrophomonas maltophilia: a crystallization contaminant identified by molecular replacement using the entire Protein Data Bank

(2016) Ronan Keegan et al.   Acta Crystallographica Section D-Structural Biology

Determination of crystal structures of proteins of unknown identity using a marathon molecular replacement procedure: structure ofStenotrophomonas maltophiliaphosphate-binding protein

(2016) Kaushik Hatti et al.   Acta Crystallographica Section D-Structural Biology

Structure of the E. coli ribosome–EF-Tu complex at

(2015) Niels Fischer et al.   NATURE

Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles

(2015) Tanmay A. M. Bharat et al.   NATURE

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

(2015) Sameer Velankar et al.   NUCLEIC ACIDS RESEARCH

Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams

(2015) Sabine Botha et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

(2015) Alan Brown et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

MoRDa, an automatic molecular replacement pipeline

(2015) Alexey Vagin et al.   Acta Crystallographica A-Foundation and Advances

ThePDB_REDOserver for macromolecular structure model optimization

(2014) Robbie P. Joosten et al.   IUCrJ

Molecular replacement: tricks and treats

(2013) Chantal Abergel   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Quantifying the local resolution of cryo-EM density maps

(2013) Alp Kucukelbir et al.   NATURE METHODS

The crystal structure analysis of the relative binding of cisplatin and carboplatin in a mixture with histidine in a protein studied at 100 and 300 K with repeated X-ray irradiation

(2012) John R. Helliwell et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

iMOSFLM: a new graphical interface for diffraction-image processing withMOSFLM

(2011) T. Geoff G. Battye et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

REFMAC5 for the refinement of macromolecular crystal structures

(2011) Garib N. Murshudov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Protein structure determination by exhaustive search of Protein Data Bank derived databases

(2010) I. Stokes-Rees et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA