VoroMQA: Assessment of protein structure quality using interatomic contact areas

ProQ2: estimation of model accuracy implemented in Rosetta

(2016) Karolis Uziela et al.   BIOINFORMATICS

Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein–protein docking results

(2016) Rahim Jafari et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Assessment of template-based modeling of protein structure in CASP11

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

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

(2016) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Estimation of Uncertainties in the Global Distance Test (GDT_TS) for CASP Models

(2016) Wenlin Li et al.   PLoS One

Benchmarking Deep Networks for Predicting Residue-Specific Quality of Individual Protein Models in CASP11

(2016) Tong Liu et al.   Scientific Reports

Protein single-model quality assessment by feature-based probability density functions

(2016) Renzhi Cao et al.   Scientific Reports

A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11

(2015) Jilong Li et al.   BMC BIOINFORMATICS

Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction

(2015) Myong-Ho Chae 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

ProQM-resample: improved model quality assessment for membrane proteins by limited conformational sampling

(2014) Björn Wallner   BIOINFORMATICS

Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls

(2014) Kliment Olechnovič et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

VLDP web server: a powerful geometric tool for analysing protein structures in their environment

(2013) Jérémy Esque et al.   NUCLEIC ACIDS RESEARCH

CAD-score: A new contact area difference-based function for evaluation of protein structural models

(2013) Kliment Olechnovič et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Delaunay-based nonlocal interactions are sufficient and accurate in protein fold recognition

(2013) Mehdi Mirzaie et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

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

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

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

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

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

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

(2011) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure

(2010) K. Olechnovic et al.   BIOINFORMATICS

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

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction-Round VIII

(2009) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

Voronoia: analyzing packing in protein structures

(2008) K. Rother et al.   NUCLEIC ACIDS RESEARCH

Specific interactions for ab initio folding of protein terminal regions with secondary structures

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing

(2007) Mingyang Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

QMEAN: A comprehensive scoring function for model quality assessment

(2007) Pascal Benkert et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE