Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta

Computational eco-systems biology in Tara Oceans: translating data into knowledge

(2015) S. Sunagawa et al.   Molecular Systems Biology

Tara Oceans studies plankton at planetary scale

(2015) P. Bork et al.   SCIENCE

Large-scale determination of previously unsolved protein structures using evolutionary information

(2015) Sergey Ovchinnikov et al.   eLife

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

Assessment of the assessment: Evaluation of the model quality estimates in CASP10

(2013) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

The Protein Model Portal—a comprehensive resource for protein structure and model information

(2013) Juergen Haas et al.   Database-The Journal of Biological Databases and Curation

Improved model quality assessment using ProQ2

(2012) Arjun Ray et al.   BMC BIOINFORMATICS

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

(2011) Y. Yang et al.   BIOINFORMATICS

GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

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

(2011) Michael Remmert et al.   NATURE METHODS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

Evaluation of model quality predictions in CASP9

(2011) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Incorporation of evolutionary information into Rosetta comparative modeling

(2011) James Thompson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Exploring protein fitness landscapes by directed evolution

(2009) Philip A. Romero et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structure prediction for CASP8 with all-atom refinement using Rosetta

(2009) Srivatsan Raman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network

(2008) Eshel Faraggi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS