LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins

ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks

(2019) Yang Li et al.   BIOINFORMATICS

Protein threading using residue co-variation and deep learning

(2018) Jianwei Zhu et al.   BIOINFORMATICS

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

Evaluation of the template-based modeling in CASP12

(2017) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

(2015) Armin Meier et al.   PLoS Computational Biology

3Dmol.js: molecular visualization with WebGL

(2014) N. Rego et al.   BIOINFORMATICS

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

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

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

(2013) Dong Xu et al.   BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP) - round x

(2013) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

(2012) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

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

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

(2011) Michael Remmert et al.   NATURE METHODS

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

(2010) Jinrui Xu et al.   BIOINFORMATICS

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

Profile Comparer: a program for scoring and aligning profile hidden Markov models

(2008) M. Madera   BIOINFORMATICS

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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