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

ProQ2: estimation of model accuracy implemented in Rosetta

(2016) Karolis Uziela et al.   BIOINFORMATICS

Evaluation of free modeling targets in CASP11 and ROLL

(2016) Lisa N. Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP 11 target classification

(2016) Lisa N. Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function

(2015) Michal J. Pietal et al.   BIOINFORMATICS

Template-free modeling by LEE and LEER in CASP11

(2015) InSuk Joung et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accurate contact predictions using covariation techniques and machine learning

(2015) Tomasz Kosciolek et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Analysis of free modeling predictions by RBO aleph in CASP11

(2015) Mahmoud Mabrouk 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

Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway

(2015) Joana Fraga 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

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network

(2014) James Lyons et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts

(2014) Tomasz Kosciolek et al.   PLoS One

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts

(2014) W. Boomsma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PconsC: combination of direct information methods and alignments improves contact prediction

(2013) Marcin J. Skwark et al.   BIOINFORMATICS

Predicting protein contact map using evolutionary and physical constraints by integer programming

(2013) Z. Wang et al.   BIOINFORMATICS

Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry

(2013) W. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

(2013) Yang Zhang   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure modeling for CASP10 by multiple layers of global optimization

(2013) Keehyoung Joo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Definition and classification of evaluation units for CASP10

(2013) Todd J. Taylor 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

Evaluation of residue-residue contact prediction in CASP10

(2013) Bohdan Monastyrskyy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting protein residue–residue contacts using deep networks and boosting

(2012) Jesse Eickholt et al.   BIOINFORMATICS

GuiTope: an application for mapping random-sequence peptides to protein sequences

(2012) Rebecca F Halperin et al.   BMC BIOINFORMATICS

Fast algorithm for population-based protein structural model analysis

(2012) Jingfen Zhang et al.   PROTEOMICS

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

A protein-dependent side-chain rotamer library

(2011) Md Shariful Bhuyan et al.   BMC BIOINFORMATICS

Protein 3D Structure Computed from Evolutionary Sequence Variation

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

An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression

(2011) Arvind Marathe et al.   BMC STRUCTURAL BIOLOGY

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

(2010) Jinrui Xu et al.   BIOINFORMATICS

Detection of gene pathways with predictive power for breast cancer prognosis

(2010) Shuangge Ma et al.   BMC BIOINFORMATICS

Sampling Bottlenecks in De novo Protein Structure Prediction

(2009) David E. Kim et al.   JOURNAL OF MOLECULAR BIOLOGY

NNcon: improved protein contact map prediction using 2D-recursive neural networks

(2009) A. N. Tegge et al.   NUCLEIC ACIDS RESEARCH

Restriction versus guidance in protein structure prediction

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

MUFOLD: A new solution for protein 3D structure prediction

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

FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps

(2008) Marco Vassura et al.   BIOINFORMATICS

Fast procedure for reconstruction of full-atom protein models from reduced representations

(2008) Piotr Rotkiewicz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A generative, probabilistic model of local protein structure

(2008) Wouter Boomsma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discriminative learning for protein conformation sampling

(2008) Feng Zhao et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS