Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12

ResQ: An Approach to Unified Estimation of B -Factor and Residue-Specific Error in Protein Structure Prediction

(2016) Jianyi Yang et al.   JOURNAL OF MOLECULAR BIOLOGY

Evaluation of free modeling targets in CASP11 and ROLL

(2016) Lisa N. Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of template-based modeling of protein structure in CASP11

(2016) Vivek Modi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2016) Sergey Ovchinnikov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade

(2015) Jianyi Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11

(2015) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11

(2015) Wenxuan Zhang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

New encouraging developments in contact prediction: Assessment of the CASP11 results

(2015) Bohdan Monastyrskyy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

(2014) Stefan Seemayer et al.   BIOINFORMATICS

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

(2014) C. N. Magnan et al.   BIOINFORMATICS

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

FreeContact: fast and free software for protein contact prediction from residue co-evolution

(2014) László Kaján et al.   BMC BIOINFORMATICS

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts

(2014) Tomasz Kosciolek et al.   PLoS One

ThreaDom: extracting protein domain boundary information from multiple threading alignments

(2013) Zhidong Xue et al.   BIOINFORMATICS

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

Toward optimal fragment generations forab initioprotein structure assembly

(2013) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

(2013) Yang Zhang   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of template-free modeling in CASP10 and ROLL

(2013) Chin-Hsien Tai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of template-based protein structure predictions in CASP10

(2013) Yuanpeng J. Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

(2013) Renxiang Yan et al.   Scientific Reports

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization

(2011) Dong Xu et al.   BIOPHYSICAL JOURNAL

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

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

CASP9 assessment of free modeling target predictions

(2011) Lisa Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of template based protein structure predictions in CASP9

(2011) Valerio Mariani et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving Protein Structure Prediction Using Multiple Sequence-Based Contact Predictions

(2011) Sitao Wu et al.   STRUCTURE

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

(2011) Jian Zhang et al.   STRUCTURE

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

(2010) Jian Zhang et al.   PLoS One

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks

(2009) Yunqi Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

I-TASSER: Fully automated protein structure prediction in CASP8

(2009) Yang Zhang   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction

(2008) Sitao Wu et al.   BIOINFORMATICS

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA