EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction

K Stahl, M Schneider, O Brock - BMC bioinformatics, 2017 - Springer
Background Accurately predicted contacts allow to compute the 3D structure of a protein.
Since the solution space of native residue-residue contact pairs is very large, it is necessary …

Combining physicochemical and evolutionary information for protein contact prediction

M Schneider, O Brock - PloS one, 2014 - journals.plos.org
We introduce a novel contact prediction method that achieves high prediction accuracy by
combining evolutionary and physicochemical information about native contacts. We obtain …

Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17)

S Pramanik, A Kutzner, K Heese - Tumor Biology, 2015 - Springer
Abstract FAM72A (p17) is a novel neuronal protein that has been linked to tumorigenic
effects in non-neuronal tissue. Using state of the art in silico physicochemical analyses (eg, I …

Membrane protein contact and structure prediction using co-evolution in conjunction with machine learning

PL Teixeira, JL Mendenhall, S Heinze, B Weiner… - Plos one, 2017 - journals.plos.org
De novo membrane protein structure prediction is limited to small proteins due to the
conformational search space quickly expanding with length. Long-range contacts (24+ …

[HTML][HTML] Predictor de interacciones entre estructuras secundarias de proteínas

JC Quintana-Zaez, N Quintana-Bernabé… - Revista Cubana de …, 2017 - scielo.sld.cu
Resumen QUINTANA-ZAEZ, Julio César et al. Predictor de interacciones entre estructuras
secundarias de proteínas. Rev cuba cienc informat [online]. 2017, vol. 11, n. 3, pp. 105-113 …

[PDF][PDF] Leveraging novel information sources for protein structure prediction

M Bohlke-Schneider - 2016 - depositonce.tu-berlin.de
Three-dimensional protein structures are an invaluable step** stone towards the
understanding of cellular processes. Computational protein structure prediction holds the …

[BOOK][B] A novel approach to de novo protein structure prediction using knowledge based energy functions and experimental restraints

N Wotzel - 2011 - search.proquest.com
The focus of this work was to develop a method for rapid fitting of atomic resolution structural
models into medium resolution electron density maps and Bayesian energy potentials for a …

[HTML][HTML] Tree-based Secondary Structure Interactions Predictor Method for Protein Contact Maps

JC Quintana-Zaez, R Molina-Ruiz… - Computación y …, 2018 - scielo.org.mx
Understanding the folding of proteins is one of the most interesting research field for the
Bioinformatics. The contact maps constitute an intermediate step in the prediction of the 3D …

[PDF][PDF] Predicting protein contacts by combining information from sequence and physicochemistry

GPDO Brock, KR Müller, BPDO Brock… - static.tu.berlin
Different kinds of information are used in contact prediction, eg, structure-based,
coevolutionary or sequence-based information. They have inherent specific strengths and …

Using Evolutionarily-Based Correlation Measures and Machine Learning to Improve Protein Structure Prediction in BCL:: Fold

PL Teixeira Jr - 2014 - ir.vanderbilt.edu
De novo protein structure prediction is a challenge due to the sheer size of the search
space. One can limit the set of potential models with long-range contact restraints (positions …