4.3 Article Proceedings Paper

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

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Editorial Material Biochemistry & Molecular Biology

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

Shinichi Sunagawa et al.

MOLECULAR SYSTEMS BIOLOGY (2015)

Editorial Material Multidisciplinary Sciences

Tara Oceans studies plankton at PLANETARY SCALE

P. Bork et al.

SCIENCE (2015)

Article Biochemical Research Methods

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

Baris E. Suzek et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Relaxation of backbone bond geometry improves protein energy landscape modeling

Patrick Conway et al.

PROTEIN SCIENCE (2014)

Article Biochemistry & Molecular Biology

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

Andriy Kryshtafovych et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

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

Hetunandan Kamisetty et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemistry & Molecular Biology

High-Resolution Comparative Modeling with RosettaCM

Yifan Song et al.

STRUCTURE (2013)

Article Mathematical & Computational Biology

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

Juergen Haas et al.

Database-The Journal of Biological Databases and Curation (2013)

Article Biochemical Research Methods

Improved model quality assessment using ProQ2

Arjun Ray et al.

BMC BIOINFORMATICS (2012)

Article Biochemical Research Methods

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

Michael Remmert et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Template-based protein structure modeling using the RaptorX web server

Morten Kaellberg et al.

NATURE PROTOCOLS (2012)

Letter Biochemical Research Methods

SignalP 4.0: discriminating signal peptides from transmembrane regions

Thomas Nordahl Petersen et al.

NATURE METHODS (2011)

Article Multidisciplinary Sciences

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

Dominik Gront et al.

PLOS ONE (2011)

Article Biochemistry & Molecular Biology

Evaluation of model quality predictions in CASP9

Andriy Kryshtafovych et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Incorporation of evolutionary information into Rosetta comparative modeling

James Thompson et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Learning generative models for protein fold families

Sivaraman Balakrishnan et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)

Article Biochemical Research Methods

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biochemical Research Methods

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

Jinrui Xu et al.

BIOINFORMATICS (2010)

Review Cell Biology

Exploring protein fitness landscapes by directed evolution

Philip A. Romero et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Structure prediction for CASP8 with all-atom refinement using Rosetta

Srivatsan Raman et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)

Review Biotechnology & Applied Microbiology

Next-generation DNA sequencing

Jay Shendure et al.

NATURE BIOTECHNOLOGY (2008)

Article Biochemistry & Molecular Biology

Prediction of structures of multidomain proteins from structures of the individual domains

Andrew M. Wollacott et al.

PROTEIN SCIENCE (2007)

Article Multidisciplinary Sciences

Toward high-resolution de novo structure prediction for small proteins

P Bradley et al.

SCIENCE (2005)

Article Biochemical Research Methods

Protein homology detection by HMM-HMM comparison

J Söding

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments

HY Zhou et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM

DE Kim et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Article Biochemical Research Methods

The DISOPRED server for the prediction of protein disorder

JJ Ward et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

Protein structure prediction and analysis using the Robetta server

DE Kim et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

LGA: a method for finding 3D similarities in protein structures

A Zemla

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemical Research Methods

MaxSub: an automated measure for the assessment of protein structure prediction quality

N Siew et al.

BIOINFORMATICS (2000)