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biophysics
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Static properties of leaves with parallel venation, with particular emphasis on the genus EpipactisZinn, 1757 (Orchidaceae, Neottieae) have been modelled with coupled quasi-parallel elastic “beams.” The non-linear theory of strongly bended beams have been employed....

["Agricultural Science","Biophysics","Mathematical Biology","Plant Science"]
doi:10.7717/peerj.2165
2 downloads
54 views

We present a rationale and proposed approach to the modification and development of bind sites using their respective cognate ligands as template. This is in support of a plausible “instructive” role for the ligand and therefore its involvement in determination...

["Biochemistry","Bioengineering","Biophysics","Biotechnology","Molecular Biology"]
doi:10.7287/peerj.preprints.2161v1
8 downloads
61 views

Design and production of polypeptide/proteins with desired bind site properties involves utilization of the ligand of interest in selection of those bind sites that yield the desired properties from an assortment bind sites with different structures and properties....

["Biochemistry","Bioengineering","Biophysics","Biotechnology"]
doi:10.7287/peerj.preprints.2160v1
53 downloads
670 views

Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the...

["Biochemistry","Biophysics","Computational Biology","Molecular Biology"]
doi:10.7717/peerj.2136
53 downloads
182 views

Metabolomic profiling is an increasingly important method for identifying potential biomarkers in cancer cells with a view towards improved diagnosis and treatment. Nuclear magnetic resonance (NMR) provides a potentially noninvasive means to accurately characterize...

["Biophysics","Metabolic Sciences"]
doi:10.7717/peerj.2104
370 downloads
475 views

History is often thought to be dull and boring – where large numbers of facts are memorized for passing exams. But the past informs the present and future, especially in delineating the context surrounding specific events that, in turn, help provide a deeper understanding...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.552v4
95 downloads
406 views

Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the...

["Biophysics","Pharmacology","Computational Science"]
doi:10.7717/peerj.2088
3 downloads
64 views

Bacteria surface charge derives its meaning from the cell’s environment; thus, there is no one specific surface charge. Determining the surface charge of bacteria in its native environment requires measuring the proxy variable, zeta potential, using cells obtained...

["Bioengineering","Biophysics","Biotechnology","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.2086v1
80 downloads
284 views

The PM6 semiempirical method and the dispersion and hydrogen bond-corrected PM6-D3H+ method are used together with the SMD and COSMO continuum solvation models to predict pKa values of pyridines, alcohols, phenols, benzoic acids, carboxylic acids, and phenols using...

["Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.2075v1
577 downloads
420 views

The past influence the present and future; for example, in computational chemistry, simplifying assumptions and approximations important to problem solving in the pre-computing era remains relevant today in allowing simulation of larger systems with reasonable...

["Biochemistry","Bioengineering","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.365v2
18 downloads
132 views

1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozyme and has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability...

["Biochemistry","Biophysics"]
doi:10.7287/peerj.preprints.1989v2
74 downloads
475 views

We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory,...

["Biophysics","Computational Biology"]
doi:10.7717/peerj.1994
48 downloads
255 views

Contrary to the majority of the members of the lipocalin family, which are stable monomers with the specific OBP fold (a β-barrel consisting of a 8-stranded anti-parallel β-sheet followed by a short α-helical segment, a ninth β-strand, and a disordered C-terminal...

["Biochemistry","Biophysics","Molecular Biology"]
doi:10.7717/peerj.1642
2 citations
36 downloads
215 views

In a family of monomeric odorant-binding proteins (OBPs), bovine OBP (bOBP), that lacks conserved disulfide bond found in other OBPs, occupies unique niche because of its ability to form domain-swapped dimers. In this study, we analyzed conformational stabilities...

["Biochemistry","Bioinformatics","Biophysics","Molecular Biology"]
doi:10.7717/peerj.1574
2 citations
50 downloads
260 views

Bovine odorant-binding protein (bOBP) differs from other lipocalins by lacking the conserved disulfide bond and for being able to form the domain-swapped dimers. To identify structural features responsible for the formation of the bOBP unique dimeric structure...

["Biochemistry","Biophysics","Molecular Biology"]
doi:10.7717/peerj.1933

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