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PCE: web tools to compute protein continuum electrostatics

M. A. Miteva, P. Tuffery, B. O. Villoutreix
2005 Nucleic Acids Research  
PCE (protein continuum electrostatics) is an online service for protein electrostatic computations presently based on the MEAD (macroscopic electrostatics with atomic detail) package initially developed  ...  This service is intended to facilitate electrostatics analyses of proteins and thereby broaden the accessibility to continuum electrostatics to the biological community. PCE can be accessed at  ...  The basic electrostatic property that can be calculated via PCE (protein continuum electrostatics) is the electrostatic potential, yet continuum electrostatic models have also proven to be useful for the  ... 
doi:10.1093/nar/gki365 pmid:15980492 pmcid:PMC1160126 fatcat:aawzg3yopzacffa6mzlqkc7wia

Electrostatics calculations: latest methodological advances

Patrice Koehl
2006 Current Opinion in Structural Biology  
• 79 . 79 Miteva MA, Tuffery P, Villoutreix BO: PCE: web tools to compute protein continuum electrostatics. Nucleic Acids Res 2005, 33:W372-W375.  ...  PCE is a web server that provides access to the MEAD package (see [80]) for computing biomolecular electrostatics properties, such as pK a values and electrostatic potentials.  ... 
doi:10.1016/j.sbi.2006.03.001 pmid:16540310 fatcat:nabd5dqrejdppfxuh4kce3lm7m

webPIPSA: a web server for the comparison of protein interaction properties

S. Richter, A. Wenzel, M. Stein, R. R. Gabdoulline, R. C. Wade
2008 Nucleic Acids Research  
the use of PIPSA to compare and analyze protein electrostatic potentials.  ...  With input protein coordinates, the superposition of protein structures, as well as the computation and analysis of electrostatic potentials, is automated.  ...  We thank Nils Semmelrock and Bruno Besson for helping to implement early versions of this software.  ... 
doi:10.1093/nar/gkn181 pmid:18420653 pmcid:PMC2447742 fatcat:fwy62pn6yreypi22dcfhmp5fta

PBEQ-Solver for online visualization of electrostatic potential of biomolecules

Sunhwan Jo, Miklos Vargyas, Judit Vasko-Szedlar, Benoît Roux, Wonpil Im
2008 Nucleic Acids Research  
PBEQ-Solver provides a web-based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential.  ...  PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein-protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue.  ...  ACKNOWLEDGEMENTS The authors are grateful to Martin Karplus for his support, to Nathan Baker for sharing useful information and to Michael Feig for sharing the results of other PB programs.  ... 
doi:10.1093/nar/gkn314 pmid:18508808 pmcid:PMC2447802 fatcat:luwhnyifnvdjtm7mlizlacmelm

Physical Properties of Intact Proteins May Predict Allergenicity or Lack Thereof

Suchita Singh, Bhupesh Taneja, Sundeep Santosh Salvi, Anurag Agrawal, Dominik Hartl
2009 PLoS ONE  
It may be possible to predict reduced likelihood of allergenicity in such proteins, but this needs to be prospectively validated.  ...  Thus neutral to basic pI, positive charge, and positive electrostatic potentials characterize non-allergens, and seem rare in allergens (p,0.0001).  ...  Calculation of electrostatic potential (EP) Surface electrostatic potential was measured through online calculation by Protein Continuum electrostatics (PCE) web tool presently based on MEAD (macroscopic  ... 
doi:10.1371/journal.pone.0006273 pmid:19609445 pmcid:PMC2707619 fatcat:6pi4xqkrxve6jcepxk6hglnwgy

Identification of B Cell Epitopes of Alcohol Dehydrogenase Allergen of Curvularia lunata

Smitha Nair, Neetu Kukreja, Bhanu Pratap Singh, Naveen Arora, Marco Idzko
2011 PLoS ONE  
Method: B cell epitopes of ADH were predicted by sequence and structure based methods and protein-protein interaction tools while T cell epitopes by inhibitory concentration and binding score methods.  ...  The computational methods employed were validated using Bet v 1 and Der p 2 allergens where 67% and 60% of the epitope residues were predicted correctly.  ...  Electrostatic potential for the protein was calculated by Protein continuum electrostatics (PCE) tool (http://bioserv.rpbs. jussieu.fr/cgi-bin/PCE-Pot) based on the MEAD (macroscopic electrostatics with  ... 
doi:10.1371/journal.pone.0020020 pmid:21647452 pmcid:PMC3102081 fatcat:lknh6ojuf5b2rg6tzmavlwaadu

A Network-based Analysis of Polyanion-binding Proteins Utilizing Human Protein Arrays

Nazila Salamat-Miller, Jianwen Fang, Christopher W. Seidel, Yassen Assenov, Mario Albrecht, C. Russell Middaugh
2007 Journal of Biological Chemistry  
The abbreviations used are: HS, heparan sulfate; PABP, polyanion-binding protein; MES, 2-(N-morpholino)ethanesulfonic acid; PCE, protein continuum electrostatics; ORF, open reading frame.  ...  The existence of protein arrays, with a large selection of different kinds of proteins, provides a way to better address a number of aspects of this question.  ...  Maria Miteva is acknowledged for help with PCE calculations.  ... 
doi:10.1074/jbc.m610957200 pmid:17276992 fatcat:qa7bhlcds5hv3cga7h6iduawme

Thiol redox biochemistry: insights from computer simulations

Ari Zeida, Carlos M. Guardia, Pablo Lichtig, Laura L. Perissinotti, Lucas A. Defelipe, Adrián Turjanski, Rafael Radi, Madia Trujillo, Darío A. Estrin
2014 Biophysical Reviews  
In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of selected relevant issues in thiol redox biochemistry, such as investigations  ...  Thiol redox chemical reactions play a key role in a variety of physiological processes, mainly due to the presence of low-molecular-weight thiols and cysteine residues in proteins involved in catalysis  ...  Many software packages are available for calculating pKa shifts, including the MEAD package and the PCE web tool (Bashford and Karplus 1990; Sanchez et al. 2008; Salsbury et al. 2012a ).  ... 
doi:10.1007/s12551-013-0127-x pmid:28509962 pmcid:PMC5427810 fatcat:ikjci7caufbspl5lfjoldnswvy

In Silico Mechanistic Profiling to Probe Small Molecule Binding to Sulfotransferases

Virginie Y. Martiny, Pablo Carbonell, David Lagorce, Bruno O. Villoutreix, Gautier Moroy, Maria A. Miteva, Daniel S. Sem
2013 PLoS ONE  
To the best of our knowledge our protocol is the first in silico structure-based approach consisting of a protein-ligand interaction analysis at atomic level that considers both ligand and enzyme flexibility  ...  Here we report a novel in silico structure-based approach to probe ligand binding to SULTs.  ...  The pK a values of titratable groups were calculated with the Finite Difference Poisson Boltzman approach [63] using the web server tool Protein Continuum Electrostatics (PCE) [64] with the default  ... 
doi:10.1371/journal.pone.0073587 pmid:24039991 pmcid:PMC3765257 fatcat:nuh4s5jcnncyrk3vwglvkfwqla

Liprotides: a New Class of Protein Lipid-Complexes

Jannik N. Pedersen, Henriette Kristina S. Frislev, Jan S. Pedersen, Daniel E. Otzen
2016 Biophysical Journal  
Many ATSAS programs have online interfaces that can be accessed through a web-browser [5].  ...  These publications cover a wide range of science, such as proteins, polymers, metallurgy, coatings, fibres, liquid crystals, and foodstuffs, and various in situ conditions including temperature, pressure  ...  Here we present a new version of DARA, a web-server that queries over 150 000 scattering patterns pre-computed from the high resolution structures of macromolecules and biological assemblies in the Protein  ... 
doi:10.1016/j.bpj.2015.11.3085 fatcat:eqeeb47atfc4lisnurb25n55gu

Characterization of Transport and Adsorption Mechanisms in Chromatographic Media

Florian Dismer
2009
The second part of this work deals with confocal laser-scanning microscopy as a tool to visualize protein transpiort in chromatographic media.  ...  Findings were correlated with molecular dynamics simulations and used to obtain a model approach to predict protein retention times in ion-exchange chromatography.  ...  This work was supported by grants from Protein Engineering Network of Centres of Excellence (PENCE) and NSERC.  ... 
doi:10.5445/ir/1000015816 fatcat:iz7t23rt3jdupfgjgousum7vlu

Plasmonic sensing through bioconjugation of Ag nanoparticles: Towards the development of immunoassays for ultralow quantification of antigens in colloidal dispersions

Pablo A. Mercadal, Juan C. Fraire, Rubén Motrich, Eduardo A. Coronado
2018 Advanced Materials Letters  
Piezoelectric, polymers or magneto resistive layers can be added to expand the options of silicon. In the case of some implants, the polymer is used to protect the body from the device.  ...  However, in some applications an addition layer may be required for sensing and/or to protect the silicon device.  ...  Also thanks to the colleagues who provided some of the figures.  ... 
doi:10.5185/amlett.2018.2001 fatcat:san2f55iwnakbgtkeet5x4pd6i

Molecular Modeling of Membrane Embedded Proteins

Thomas Lemmin
2013
Neural Plasticity and Repair (to P.C.F.), the Strauss foundation (to P.C.F.), and an EPFL-Merck-Serono grant (to J.R.A. and M.D.).  ...  ACKNOWLEDGEMENTS We are very grateful to the patients and their parents for accepting to be part of this study and for their collaborative attitude.  ...  This solvent approximation, where the water molecules are described as a dielectric continuum, considerably reduces the computational time, allowing to reach hundreds of ns long simulations.  ... 
doi:10.5075/epfl-thesis-5695 fatcat:kuyc2ht43bdwljrtsmyodzffjy

Effects of monoamine releasers with varying selectivity for releasing dopamine/norepinephrine versus serotonin on choice between cocaine and food in rhesus monkeys

Matthew L. Banks, Bruce E. Blough, S. Stevens Negus
2011 Behavioural Pharmacology  
Together, these data implicate the amygdala as a key region modulating the appetitive properties of nicotine, and suggest that κ-opioid antagonists may be useful therapeutic tools to reduce stress-induced  ...  Serine 77 In The PDZ Domain Of PICK1 Is A Protein Kinase Cα Phosphorylation Site Regulated By Lipid Membrane Binding PICK1 (protein interacting with C kinase 1) contains an N-terminal protein binding PDZ  ...  necessary to facilitate their implementation in these new contexts; and (3) novel service delivery models to be pilot tested in preparation for larger-scale effectiveness trials.  ... 
doi:10.1097/fbp.0b013e32834d63ac pmid:22015808 pmcid:PMC3476464 fatcat:wxbgqsqazfegvfnvq6gdvwreua