Accurate Prediction of Contact Numbers for Multi-Spanning Helical #MembraneProteins – via #NeuralNetwork w/ dropout
http://pubs.ACS.org/doi/abs/10.1021/acs.jcim.5b00517 In turn, this can enable accurate prediction of the rotation of TM helices & then the 3D #StructurePrediction of the whole protein
Posts Tagged ‘pda’
Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins
November 25, 2017PLOS Computational Biology: PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations
November 28, 2016PredictSNP…Consensus Classifier for Prediction of Disease-Related
Mutations http://journals.PLOS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003440 Demo of various #ensemble approaches
PLOS Computational Biology: PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions
October 9, 2016PredictSNP2: A Unified Platform http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004962 Ensembles many scores for the impact of non-coding variants, including #FunSeq
Elucidating Molecular Motion through Structural and Dynamic Filters of Energy-Minimized Conformer Ensembles
September 30, 2016Elucidating Molecular Motion (compatible w. #NMR relaxation times) through…Filters of Energy-Minimized…Ensembles
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983377
Spatial confinement is a major determinant of the folding landscape of human chromosomes
July 28, 2016Gamze Gursoy, Yun Xu, Amy Kenter and Jie Liang. “Spatial confinement is a major determinant of folding landscape of human genome”, Nucleic Acids Research, 2014, 42 (13), 8223-8230
Confinement is a major determinant of the #folding…of chromosomes http://NAR.oxfordjournals.org/content/42/13/8223.full Simulations of self-avoiding chain growth
Predicting peptide binding sites on protein surfaces by clustering chemical interactions – Yan – 2014 – Journal of Computational Chemistry – Wiley Online Library
July 4, 2016Predicting peptide binding sites on protein surfaces by ACCLUSTER http://onlinelibrary.wiley.com/doi/10.1002/jcc.23771/abstract #Chemical interactions out perform pure #packing
Protein folds recognized by an intelligent predictor based-on evolutionary and structural information – Cheung – 2015 – Journal of Computational Chemistry – Wiley Online Library
April 17, 2016Fold [class] recognized by an…[NN] predictor based-on evolutionary & structural info., w/ particle-swarm training
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24232/full
Ngaam J. Cheung,
Xue-Ming Ding,
Hong-Bin Shen
First published: 27 October 2015
DOI: 10.1002/jcc.24232
PLOS Computational Biology: Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations
December 18, 2015Folding by Chaperones Accelerates Evolutionary Dynamics
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003269 Multiscale models link NT mutations, PPIs & cell populations
Thermodynamics of Antimicrobial Lipopeptide Binding to Membranes: Origins of Affinity and Selectivity: Biophysical Journal
November 15, 2015#Thermodynamics of Antimicrobial Lipopeptide Binding to Membranes http://www.cell.com/biophysj/abstract/S0006-3495(14)00928-X Non-human selectivity studied w. coarse-grained MD
A Multiscale Coarse-Graining Method for Biomolecular Systems – The Journal of Physical Chemistry B (ACS Publications)
November 15, 2015A Multiscale Coarse-Graining Method for Biomolecul[es] http://pubs.acs.org/doi/abs/10.1021/jp044629q Simplified force field from fitting to all-atom #simulations
Sergei Izvekov and Gregory A. Voth *
J. Phys. Chem. B, 2005, 109 (7), pp 2469–2473
DOI: 10.1021/jp044629q
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