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biophysics
5 downloads
90 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
551 downloads
394 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
16 downloads
125 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
62 downloads
361 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
42 downloads
213 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
34 downloads
183 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
42 downloads
211 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
10 downloads
55 views

It is well known that the biological properties of compounds are directly related to the configuration of their stereogenic centers. Therefore, the determination of the compound spatial structure, including its configuration, is crucial for better understanding...

["Biophysics","Drugs and Devices","Science and Medical Education"]
doi:10.7287/peerj.preprints.1935v1
86 downloads
219 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:10.7287/peerj.preprints.1931v1
18 downloads
49 views

The attractor method and some of its applications are presented. We start with the original research question “How to diagnose fatigue (fatigability) in MS patients reliably”. So far a decisive method to discriminate between non-fatiguing and marginal fatiguing...

["Biophysics","Neuroscience","Kinesiology","Computational Science"]
doi:10.7287/peerj.preprints.1822v1
101 downloads
510 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:10.7287/peerj.preprints.1741v2
158 downloads
731 views

The 2014 Ebola virus (EBOV) outbreak in West Africa is the largest in recorded history and resulted in over 11,000 deaths. It is essential that strategies for treatment and containment be developed to avoid future epidemics of this magnitude. With the development...

["Biophysics","Evolutionary Studies","Molecular Biology","Virology","Infectious Diseases"]
doi:10.7717/peerj.1674
35 downloads
92 views

Here we question the generality of the conventional definition of a native conformation –as the 3-dimensional conformation of an entire globular polypeptide molecule. Although considered common knowledge, and thus not explicitly stated in modern writings, this...

["Biochemistry","Bioengineering","Biophysics","Biotechnology","Molecular Biology"]
doi:10.7287/peerj.preprints.1735v1
98 downloads
454 views

Background. Amyloid secondary structure relies on the intermolecular assembly of polypeptide chains through main-chain interaction. According to this, all proteins have the potential to form amyloid structure, nevertheless, in nature only few proteins aggregate...

["Biophysics"]
doi:10.7717/peerj.1676
100 downloads
345 views

Background/objectives. This study examines the surface activity, resistance to biophysical inhibition, and pulmonary efficacy of a synthetic lung surfactant containing glycerophospholipids combined with Super Mini-B (S-MB) DATK, a novel and stable molecular mimic...

["Bioengineering","Biophysics","Respiratory Medicine"]
doi:10.7717/peerj.1528

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