Preprints (not yet peer-reviewed)

1,010 downloads
1,815 views

Zeta potential, defined as the electric charge at the shear plane, is widely used as a proxy parameter for bacterial cell surface charge. Nonspecific adsorption of ions or polyelectrolytes onto the cell surface, however, alters the value and polarity of the measured...

["Bioengineering","Biophysics","Biotechnology","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.110v6
22 downloads
172 views

A complete understanding of the feeding structures is fundamental in order to study how animals survive. Some birds use long and protrusible tongues as the main tool to collect their central caloric source (e.g. woodpeckers and nectarivores). Hummingbirds are the...

["Biophysics","Zoology","Anatomy and Physiology"]
doi:10.7287/peerj.preprints.2986v1
178 downloads
476 views

In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for...

["Biochemistry","Bioinformatics","Biophysics","Pharmacology","Computational Science"]
doi:10.7287/peerj.preprints.2857v2
43 downloads
155 views

Membrane proteins are the most medicinally important yet to be fully exploited pharmaceutical targets. Here druggability analyses are conducted on three different membrane proteins, namely, the human P2Y12 receptor, glycoprotein-41 that mediates the HIV-1 virus...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.2868v1
23 downloads
175 views

The importance of histidine tautomerism for an accurate drug/protein structure determination and their relevance for the interaction between biological systems is recognized. Consequently, here we used a recently introduced method to determine the pKa values of...

["Bioinformatics","Biophysics","Computational Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.2816v1
30 downloads
185 views

Hydrolysis of ATP by Na+/K+-ATPase, a P-Type ATPase, catalyzing active Na+ and K+ transport through cellular membranes leads transiently to a phosphorylation of its catalytical α-subunit. Surprisingly, 3-dimensional molecular structure analysis of P-type ATPases...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2812v1
22 downloads
155 views

It is now widely accepted that oligomers consisting of Aβ peptide are the cytotoxic species contributing mostly to the development of Alzheimer’s disease. Aβ peptide production results from the specific proteolytic processing of the amyloid precursor protein (APP)....

["Biophysics","Biotechnology","Cell Biology","Molecular Biology","Neuroscience"]
doi:10.7287/peerj.preprints.2804v1
45 downloads
175 views

Without exception, modern hypotheses explaining the origin of eukaryotes assume evolution from two (or more) distinct prokaryotes. Almost all prokaryotic cell membranes possess a chemiosmosis system, whereas eukaryotic cell membranes have lost that ability. Nevertheless,...

["Biophysics","Evolutionary Studies"]
doi:10.7287/peerj.preprints.2802v1
866 downloads
778 views

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

["Biochemistry","Bioengineering","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.365v4
44 downloads
179 views

Background: Food preservation is essential to the growing world population, food economy. Freezing is a commonly used method for food preservation. While extending the life of the product, freezing has detrimental effects. It is causing loss of food weight and...

["Agricultural Science","Biophysics","Cell Biology","Food Science and Technology","Plant Science"]
doi:10.7287/peerj.preprints.2740v1
73 downloads
262 views

This document is my attempt at distilling some of the information in two papers published by Anthony Nicholls (J. Comput. Aided Mol. Des. 2014, 28, 887; ibid 2016, 30, 103). Anthony also very kindly provided some new equations, not found in the papers, in response...

["Biophysics","Computational Biology","Mathematical Biology","Computational Science"]
doi:10.7287/peerj.preprints.2693v1
12 downloads
133 views

Coral reefs are dynamic systems whose composition is highly influenced by unpredictable biotic and abiotic factors. Understanding the spatial scale at which long-term predictions of reef composition can be made will be crucial for guiding conservation efforts....

["Biophysics","Ecology","Marine Biology"]
doi:10.7287/peerj.preprints.2687v1
24 downloads
184 views

Type I restriction-modification enzymes are multisubunit, multifunctional molecular machines that recognize specific DNA target sequences, and their multisubunit organization underlies their multifunctionality. EcoR124I is the archetype of Type I restriction-modification...

["Biochemistry","Biophysics","Computational Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.2680v1
230 downloads
531 views

Rapid yet accurate pKa prediction for drug-like molecules is a key challenge in computational chemistry. This study uses PM6-DH+/COSMO, PM6/COSMO, PM7/COSMO, PM3/COSMO, AM1/COSMO, PM3/SMD, AM1/SMD, and DFTB3/SMD to predict the pKa values of 53 amine groups in 48...

["Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.2564v2
58 downloads
288 views

Background: Cryoelectrolysis is a new minimally invasive tissue ablation surgical technique that combines the ablation techniques of electrolytic ablation with cryosurgery. The goal of this study is to examine the hypothesis that electrolysis can take place in...

["Bioengineering","Biophysics","Oncology","Surgery and Surgical Specialties"]
doi:10.7287/peerj.preprints.2474v2
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