Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins

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

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement

(2015) Gábor Bunkóczi et al.   STRUCTURE

A fragmentation and reassembly method forab initiophasing

(2015) Rojan Shrestha et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Structure solution with ARCIMBOLDO using fragments derived from distant homology models

(2014) Massimo Sammito et al.   FEBS Journal

Improved estimates of coordinate error for molecular replacement

(2013) Robert D. Oeffner et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking

(2013) Dong Xu et al.   BIOINFORMATICS

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

(2013) Renxiang Yan et al.   Scientific Reports

AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computedab initiomodels

(2012) Jaclyn Bibby et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement

(2012) Marcin Pawlowski et al.   BMC BIOINFORMATICS

Improvement of molecular-replacement models withSculptor

(2011) Gábor Bunkóczi et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

Improved molecular replacement by density- and energy-guided protein structure optimization

(2011) Frank DiMaio et al.   NATURE

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

(2011) Jian Zhang et al.   STRUCTURE

Percentile-based spread: a more accurate way to compare crystallographic models

(2010) Edwin Pozharski   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

(2010) Jinrui Xu et al.   BIOINFORMATICS

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

(2009) Anna Lobley et al.   BIOINFORMATICS

X-ray structure of a soluble Rieske-type ferredoxin fromMus musculus

(2008) Elena J. Levin et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

CHAINSAW: a program for mutating pdb files used as templates in molecular replacement

(2008) Norman Stein   JOURNAL OF APPLIED CRYSTALLOGRAPHY

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information

(2008) Sitao Wu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS