Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage

Martini 3: a general purpose force field for coarse-grained molecular dynamics

(2021) Paulo C. T. Souza et al.   NATURE METHODS

A clearer picture of the ER translocon complex

(2020) Max Gemmer et al.   JOURNAL OF CELL SCIENCE

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for membrane insertion by the human ER membrane protein complex

(2020) Tino Pleiner et al.   SCIENCE

How paired PSII–LHCII supercomplexes mediate the stacking of plant thylakoid membranes unveiled by structural mass-spectrometry

(2020) Pascal Albanese et al.   Nature Communications

Membrane Thinning Induces Sorting of Lipids and the Amphipathic Lipid Packing Sensor (ALPS) Protein Motif

(2020) Niek van Hilten et al.   Frontiers in Physiology

Structural Basis of Tail-Anchored Membrane Protein Biogenesis by the GET Insertase Complex

(2020) Melanie A. McDowell et al.   MOLECULAR CELL

Single-particle cryo-EM at atomic resolution

(2020) Takanori Nakane et al.   NATURE

Atomic-resolution protein structure determination by cryo-EM

(2020) Ka Man Yip et al.   NATURE

Delayed by Design: Role of Suboptimal Signal Peptidase Processing of Viral Structural Protein Precursors in Flaviviridae Virus Assembly

(2020) Nabeel Alzahrani et al.   Viruses-Basel

An ER translocon for multi-pass membrane protein biogenesis

(2020) Philip T McGilvray et al.   eLife

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM

(2019) Mark A. Herzik et al.   Nature Communications

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning

(2019) Michael Schantz Klausen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Brief History of Protein Sorting Prediction

(2019) Henrik Nielsen et al.   PROTEIN JOURNAL

PhoX: An IMAC-Enrichable Cross-Linking Reagent

(2019) Barbara Steigenberger et al.   ACS Central Science

Real-time cryo-electron microscopy data preprocessing with Warp

(2019) Dimitry Tegunov et al.   NATURE METHODS

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Real-space refinement in PHENIX for cryo-EM and crystallography

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field

(2018) Timothy S Carpenter et al.   Journal of Chemical Theory and Computation

Efficient and robust proteome-wide approaches for cross-linking mass spectrometry

(2018) Oleg Klykov et al.   Nature Protocols

Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics

(2017) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3

(2017) Stefan Schoebel et al.   NATURE

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

(2017) Shawn Q Zheng et al.   NATURE METHODS

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

The Natural Product Cavinafungin Selectively Interferes with Zika and Dengue Virus Replication by Inhibition of the Host Signal Peptidase

(2017) David Estoppey et al.   Cell Reports

Structure and topology around the cleavage site regulate post-translational cleavage of the HIV-1 gp160 signal peptide

(2017) Erik Lee Snapp et al.   eLife

Martini straight: Boosting performance using a shorter cutoff and GPUs

(2016) Djurre H. de Jong et al.   COMPUTER PHYSICS COMMUNICATIONS

Improved Side Chain Dynamics in MARTINI Simulations of Protein–Lipid Interfaces

(2016) Florian A. Herzog et al.   Journal of Chemical Theory and Computation

Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons

(2016) Vlad Popa et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A CRISPR screen defines a signal peptide processing pathway required by flaviviruses

(2016) Rong Zhang et al.   NATURE

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

(2016) Haim Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Peptide binding to a bacterial signal peptidase visualized by peptide tethering and carrier-driven crystallization

(2016) Yi Tian Ting et al.   IUCrJ

Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles

(2015) Michael T. Marty et al.   ANALYTICAL CHEMISTRY

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

(2015) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

(2015) Alexis Rohou et al.   JOURNAL OF STRUCTURAL BIOLOGY

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis

(2015) Leandro Martínez   PLoS One

Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line

(2014) Patrick Essletzbichler et al.   GENOME RESEARCH

The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer

(2014) Richard Alexander Scheltema et al.   MOLECULAR & CELLULAR PROTEOMICS

Structural basis of Sec-independent membrane protein insertion by YidC

(2014) Kaoru Kumazaki et al.   NATURE

Novel Parallelized Quadrupole/Linear Ion Trap/Orbitrap Tribrid Mass Spectrometer Improving Proteome Coverage and Peptide Identification Rates

(2013) Michael W. Senko et al.   ANALYTICAL CHEMISTRY

Structure and mechanism of Escherichia coli type I signal peptidase

(2013) Mark Paetzel   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

Signal Peptidase Complex Subunit 1 Participates in the Assembly of Hepatitis C Virus through an Interaction with E2 and NS2

(2013) Ryosuke Suzuki et al.   PLoS Pathogens

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

Human Cytomegalovirus UL40 Signal Peptide Regulates Cell Surface Expression of the NK Cell Ligands HLA-E and gpUL18

(2012) V. Prod'homme et al.   JOURNAL OF IMMUNOLOGY

N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB

(2012) P. Van Damme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Bayesian View on Cryo-EM Structure Determination

(2011) Sjors H.W. Scheres   JOURNAL OF MOLECULAR BIOLOGY

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

A Comprehensive Comparison of Transmembrane Domains Reveals Organelle-Specific Properties

(2010) Hayley J. Sharpe et al.   CELL

The Drosophila Crumbs signal peptide is unusually long and is a substrate for signal peptide peptidase

(2010) Annett Kilic et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY