Posts Tagged ‘pda’

PLOS Computational Biology: PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

November 28, 2016

PredictSNP…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, 2016

PredictSNP2: 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, 2016

Elucidating 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, 2016

Gamze 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

http://nar.oxfordjournals.org/content/42/13/8223.full

Predicting peptide binding sites on protein surfaces by clustering chemical interactions – Yan – 2014 – Journal of Computational Chemistry – Wiley Online Library

July 4, 2016

Predicting 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, 2016

Fold [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, 2015

Folding 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, 2015

A 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

Why Human Disease-Associated Residues Appear as the Wild-Type in Other Species: Genome-Scale Structural Evidence for the Compensation Hypothesis

September 14, 2015

Why human disease-associated residues appear as WT in other species http://mbe.oxfordjournals.org/content/31/7/1787.abstract Compensation by their 3D structural neighbors