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Total of 411 results See all subject areas
computational biology

Antifreeze proteins (AFP) in living organisms play a key role in their tolerance to extremely cold temperatures and have wide range of biotechnological applications. But on account of diversity, their identification has been challenging to biologists. Earlier work...

["Computational Biology"]
doi:10.7287/peerj.preprints.224v3

The past influences the present and future; for example, in computational chemistry, simplifying assumptions and approximations critical 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.365v1

Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage these animals, more detailed treatments are often needed...

["Computational Biology","Ecology","Marine Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.364v1

We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows us to predict changes in...

["Biochemistry","Computational Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.146v4

The Data Rate Theorem that establishes a formal linkage between real-time linear control theory and information theory carries deep implications for the study of embodied cognition and its dysfunctions across human, machine, and composite man-machine cockpit entities....

["Computational Biology","Psychiatry and Psychology","Human-Computer Interaction"]
doi:10.7287/peerj.preprints.356v1

We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al with a modified version of the H+ hydrogen bond correction by...

["Biochemistry","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.353v1

scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal "Modified BSD" open source license, provides a well-documented API in the Python programming...

["Bioinformatics","Computational Biology","Computational Science","Human-Computer Interaction","Science and Medical Education"]
doi:10.7287/peerj.preprints.336v2

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7717/peerj.332

The binding of several rubromycin-based ligands to HIV1-reverse transcriptase was analyzed using molecular docking and molecular dynamics simulations. MM-PBSA analysis and examination of the trajectories allowed the identification of several promising compounds...

["Biochemistry","Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.348v1

Multiple cell types form specialized protein complexes, podosomes or invadopodia and collectively referred to as invadosomes, which are used by the cell to actively degrade the surrounding extracellular matrix. Due to their potential importance in both healthy...

["Bioengineering","Bioinformatics","Cell Biology","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.320v1

Parasite transmission in host communities is a function of ecological factors that influence interspecific contacts and contact patterns within species. These two levels are studied with different kinds of networks – ecological networks and individual contact networks...

["Computational Biology","Ecology","Epidemiology"]
doi:10.7287/peerj.preprints.307v1

The addition of two electrons and two protons to the C17=C18 bond in protochlorophyllide is catalyzed by a light-dependent enzyme relying on NADPH as electron donor, and by a light-independent enzyme bearing a (Cys)3Asp-ligated [4Fe-4S] cluster which is reduced...

["Biochemistry","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.302v1

Classification of antibody Complementarity-Determining Region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure...

["Bioinformatics","Computational Biology","Molecular Biology","Immunology"]
doi:10.7287/peerj.preprints.291v3

The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR conformation in...

["Bioinformatics","Computational Biology","Molecular Biology","Immunology"]
doi:10.7287/peerj.preprints.292v3

Many protein domains bind to short peptide sequences, called linear motifs. Data on their sequence specificities is sparse, which is why biologists usually resort to basic pattern searches to identify new putative binding sites for experimental follow-up. Most...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.315

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