The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

GLProbs: Aligning Multiple Sequences Adaptively

(2015) Yongtao Ye et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A domain dictionary of trimeric autotransporter adhesins

(2015) Jens Bassler et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

The EMBL-EBI bioinformatics web and programmatic tools framework

(2015) Weizhong Li et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Anatomy of BioJS, an open source community for the life sciences

(2015) Guy Yachdav et al.   eLife

Axial helix rotation as a mechanism for signal regulation inferred from the crystallographic analysis of the E. coli serine chemoreceptor

(2014) Hedda U. Ferris et al.   JOURNAL OF STRUCTURAL BIOLOGY

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

PredictProtein—an open resource for online prediction of protein structural and functional features

(2014) Guy Yachdav et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied toProteopedia

(2013) Robert M. Hanson et al.   ISRAEL JOURNAL OF CHEMISTRY

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

(2013) Naomi K. Fox et al.   NUCLEIC ACIDS RESEARCH

Mechanism of Regulation of Receptor Histidine Kinases

(2012) Hedda U. Ferris et al.   STRUCTURE

HHfrag: HMM-based fragment detection using HHpred

(2011) Ivan Kalev et al.   BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

GCView: the genomic context viewer for protein homology searches

(2011) I. Grin et al.   NUCLEIC ACIDS RESEARCH

The Mechanisms of HAMP-Mediated Signaling in Transmembrane Receptors

(2011) Hedda U. Ferris et al.   STRUCTURE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea

(2011) Nagarajan Paramasivam et al.   Frontiers in Microbiology

Robust probabilistic superposition and comparison of protein structures

(2010) Martin Mechelke et al.   BMC BIOINFORMATICS

Measuring the conformational space of square four-helical bundles with the program samCC

(2010) Stanislaw Dunin-Horkawicz et al.   JOURNAL OF STRUCTURAL BIOLOGY

Evolution of Outer Membrane β-Barrels from an Ancestral ββ Hairpin

(2010) M. Remmert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transmembrane protein topology prediction using support vector machines

(2009) Timothy Nugent et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

(2009) Simon W. Ginzinger et al.   JOURNAL OF BIOMOLECULAR NMR

HHomp—prediction and classification of outer membrane proteins

(2009) Michael Remmert et al.   NUCLEIC ACIDS RESEARCH

Sequence context-specific profiles for homology searching

(2009) A. Biegert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Domain annotation of trimeric autotransporter adhesins—daTAA

(2008) Pawel Szczesny et al.   BIOINFORMATICS

Prediction of protein functional residues from sequence by probability density estimation

(2008) J. D. Fischer et al.   BIOINFORMATICS

De novo identification of highly diverged protein repeats by probabilistic consistency

(2008) A. Biegert et al.   BIOINFORMATICS

PDBalert: automatic, recurrent remote homology tracking and protein structure prediction

(2008) Vatsal Agarwal et al.   BMC STRUCTURAL BIOLOGY