Random Forest-Based Protein Model Quality Assessment (RFMQA) Using Structural Features and Potential Energy Terms

Hidden Information Revealed by Optimal Community Structure from a Protein-Complex Bipartite Network Improves Protein Function Prediction

(2013) Juyong Lee et al.   PLoS One

Protein structure modeling for CASP10 by multiple layers of global optimization

(2013) Keehyoung Joo 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

Improved model quality assessment using ProQ2

(2012) Arjun Ray et al.   BMC BIOINFORMATICS

PROTS-RF: A Robust Model for Predicting Mutation-Induced Protein Stability Changes

(2012) Yunqi Li et al.   PLoS One

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

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

A Sampling-Based Method for Ranking Protein Structural Models by Integrating Multiple Scores and Features

(2011) Xiaohu Shi et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Evaluation of model quality predictions in CASP9

(2011) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8

(2010) Z. Wang et al.   BIOINFORMATICS

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

(2010) Ambrish Roy et al.   Nature Protocols

A series of PDB related databases for everyday needs

(2010) R. P. Joosten et al.   NUCLEIC ACIDS RESEARCH

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

Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments

(2009) L. J. McGuffin et al.   BIOINFORMATICS

Prediction of DNA-binding residues from protein sequence information using random forests

(2009) Liangjiang Wang et al.   BMC GENOMICS

Quality Assessment of Protein Structure Models

(2009) Daisuke Kihara et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Prediction of global and local quality of CASP8 models by MULTICOM series

(2009) Jianlin Cheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of global and local model quality in CASP8 using the ModFOLD server

(2009) Liam J. McGuffin   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust

(2009) Pascal Benkert et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of global and local model quality in CASP8 using Pcons and ProQ

(2009) Per Larsson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

I-TASSER: Fully automated protein structure prediction in CASP8

(2009) Yang Zhang   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests

(2009) Mile Šikić et al.   PLoS Computational Biology

The ModFOLD server for the quality assessment of protein structural models

(2008) L. J. McGuffin   BIOINFORMATICS

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

(2008) Yuedong Yang et al.   PROTEIN SCIENCE

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

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

Evaluating the absolute quality of a single protein model using structural features and support vector machines

(2008) Zheng Wang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

FEATURE SELECTION IN VALIDATING MASS SPECTROMETRY DATABASE SEARCH RESULTS

(2008) JIANWEN FANG et al.   Journal of Bioinformatics and Computational Biology

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

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

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