Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13

CONFOLD2: improved contact-driven ab initio protein structure modeling

(2018) Badri Adhikari et al.   BMC BIOINFORMATICS

Smooth orientation-dependent scoring function for coarse-grained protein quality assessment

(2018) Mikhail Karasikov et al.   BIOINFORMATICS

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods

(2017) Luciano A. Abriata et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age

(2017) Joerg Schaarschmidt et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

(2017) Sheng Wang et al.   PLoS Computational Biology

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

(2016) Debswapna Bhattacharya et al.   BIOINFORMATICS

ConEVA: a toolbox for comprehensive assessment of protein contacts

(2016) Badri Adhikari et al.   BMC BIOINFORMATICS

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

(2016) Renzhi Cao et al.   BMC BIOINFORMATICS

3D genome structure modeling by Lorentzian objective function

(2016) Tuan Trieu et al.   NUCLEIC ACIDS RESEARCH

3Drefine: an interactive web server for efficient protein structure refinement

(2016) Debswapna Bhattacharya et al.   NUCLEIC ACIDS RESEARCH

Evaluation of free modeling targets in CASP11 and ROLL

(2016) Lisa N. Kinch 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

ProQ3: Improved model quality assessments using Rosetta energy terms

(2016) Karolis Uziela et al.   Scientific Reports

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

(2015) Renzhi Cao et al.   BIOINFORMATICS

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

New encouraging developments in contact prediction: Assessment of the CASP11 results

(2015) Bohdan Monastyrskyy 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

CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

(2014) Stefan Seemayer et al.   BIOINFORMATICS

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

(2014) C. N. Magnan et al.   BIOINFORMATICS

FreeContact: fast and free software for protein contact prediction from residue co-evolution

(2014) László Kaján et al.   BMC 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

Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences

(2014) Magnus Ekeberg et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data

(2014) Tuan Trieu et al.   NUCLEIC ACIDS RESEARCH

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

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

(2013) Valerio Mariani et al.   BIOINFORMATICS

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

(2013) Dong Xu et al.   BIOINFORMATICS

Designing and benchmarking the MULTICOM protein structure prediction system

(2013) Jilong Li et al.   BMC STRUCTURAL BIOLOGY

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

APOLLO: a quality assessment service for single and multiple protein models

(2011) Z. Wang et al.   BIOINFORMATICS

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

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

(2011) Michael Remmert et al.   NATURE METHODS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Z. Wang et al.   BIOINFORMATICS

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

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

(2010) Ambrish Roy et al.   Nature Protocols

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

PreDisorder: ab initio sequence-based prediction of protein disordered regions

(2009) Xin Deng et al.   BMC BIOINFORMATICS

Sequence context-specific profiles for homology searching

(2009) A. Biegert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) M. Madera   BIOINFORMATICS

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

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

A multi-template combination algorithm for protein comparative modeling

(2008) Jianlin Cheng   BMC STRUCTURAL BIOLOGY

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

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

Pcons: A neural-network-based consensus predictor that improves fold recognition

(2002) Jesper Lundström et al.   PROTEIN SCIENCE