DeepQA: improving the estimation of single protein model quality with deep belief networks

UniCon3D:de novoprotein structure prediction using united-residue conformational search via stepwise, probabilistic sampling

(2016) Debswapna Bhattacharya et al.   BIOINFORMATICS

ProQ2: estimation of model accuracy implemented in Rosetta

(2016) Karolis Uziela et al.   BIOINFORMATICS

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

Integrated protein function prediction by mining function associations, sequences, and protein–protein and gene–gene interaction networks

(2016) Renzhi Cao et al.   METHODS

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

A Stochastic Point Cloud Sampling Method for Multi-Template Protein Comparative Modeling

(2016) Jilong Li et al.   Scientific Reports

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

Large-scale model quality assessment for improving protein tertiary structure prediction

(2015) Renzhi Cao et al.   BIOINFORMATICS

FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition

(2015) Chao Wang et al.   BIOINFORMATICS

3DRobot: automated generation of diverse and well-packed protein structure decoys

(2015) Haiyou Deng et al.   BIOINFORMATICS

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

Deep learning

(2015) Yann LeCun et al.   NATURE

Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11

(2015) Renzhi Cao 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

CONFOLD: Residue-residue contact-guidedab initioprotein folding

(2015) Badri Adhikari et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

De novo protein conformational sampling using a probabilistic graphical model

(2015) Debswapna Bhattacharya et al.   Scientific Reports

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines

(2014) Renzhi Cao et al.   BMC BIOINFORMATICS

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

(2014) Balachandran Manavalan et al.   PLoS One

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment

(2014) Renzhi Cao et al.   BMC STRUCTURAL BIOLOGY

Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding

(2013) Avinash Mishra et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Predicting protein residue–residue contacts using deep networks and boosting

(2012) Jesse Eickholt et al.   BIOINFORMATICS

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

MUFOLD-WQA: A new selective consensus method for quality assessment in protein structure prediction

(2011) Qingguo Wang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Raptorx: Exploiting structure information for protein alignment by statistical inference

(2011) Jian Peng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Quality assessment of protein model-structures using evolutionary conservation

(2010) Matan Kalman et al.   BIOINFORMATICS

Toward the estimation of the absolute quality of individual protein structure models

(2010) Pascal Benkert 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

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

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

MUFOLD: A new solution for protein 3D structure prediction

(2009) Jingfen Zhang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The ModFOLD server for the quality assessment of protein structural models

(2008) L. J. McGuffin   BIOINFORMATICS

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

Fragment-HMM: A new approach to protein structure prediction

(2008) Shuai Cheng Li 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