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Protein contact prediction

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https://www.readbyqxmd.com/read/28447801/droplets-on-microdecorated-surfaces-evolution-of-the-polygonal-contact-line
#1
Alok Kumar, Rishi Raj
Interaction of liquids with surfaces is ubiquitous in our physical environment as well as many engineering applications. Recent advances on this topic have not only provided us with valuable insight into nature's design, but also enabled improved fluidic manipulation for liquid-based printing applications such as bio-microarrays for protein and DNA sequencing, multicolor polymer-based LED displays, inkjet printing, and solder droplet printing, among others. For example, droplet contact lines which are typically circular on a smooth and homogenous surface when deposited on a microdecorated surface may take various common polygonal shapes such as squares, rectangles, hexagons, octagons and dodecagons...
April 27, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28447708/protein-collapse-is-encoded-in-the-folded-state-architecture
#2
Himadri S Samanta, Pavel I Zhuravlev, Michael Hinczewski, Naoto Hori, Shaon Chakrabarti, D Thirumalai
Folded states of single domain globular proteins are compact with high packing density. The radius of gyration, Rg, of both the folded and unfolded states increase as N(ν) where N is the number of amino acids in the protein. The values of the Flory exponent ν are, respectively, ≈⅓ and ≈0.6 in the folded and unfolded states, coinciding with those for homopolymers. However, the extent of compaction of the unfolded state of a protein under low denaturant concentration (collapsibility), conditions favoring the formation of the folded state, is unknown...
April 27, 2017: Soft Matter
https://www.readbyqxmd.com/read/28446903/simulating-intestinal-growth-conditions-enhances-toxin-production-of-enteropathogenic-bacillus-cereus
#3
Nadja Jeßberger, Corinna Rademacher, Viktoria M Krey, Richard Dietrich, Ann-Katrin Mohr, Maria-Elisabeth Böhm, Siegfried Scherer, Monika Ehling-Schulz, Erwin Märtlbauer
Bacillus cereus is a ubiquitous bacterial pathogen increasingly reported to be the causative agent of foodborne infections and intoxications. Since the enterotoxins linked to the diarrheal form of food poising are foremost produced in the human intestine, the toxic potential of enteropathogenic B. cereus strains is difficult to predict from studies carried out under routine cultivation procedures. In this study, toxigenic properties of a panel of strains (n = 19) of diverse origin were compared using cell culture medium pre-incubated with CaCo-2 cells to mimic intestinal growth conditions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28441034/thrombus-formation-at-high-shear-rate
#4
Lauren D C Casa, David N Ku
The final common pathway in myocardial infarction and ischemic stroke is occlusion of blood flow from a thrombus forming under high shear rates in arteries. A high-shear thrombus forms rapidly and is distinct from the slow formation of coagulation that occurs in stagnant blood. Thrombosis at high shear rates depends primarily on the long protein von Willebrand factor (vWF) and platelets, with hemodynamics playing an important role in each stage of thrombus formation, including vWF binding, platelet adhesion, platelet activation, and rapid thrombus growth...
April 24, 2017: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/28439455/the-evolution-of-logic-circuits-for-the-purpose-of-protein-contact-map-prediction
#5
Samuel D Chapman, Christoph Adami, Claus O Wilke, Dukka B Kc
Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset...
2017: PeerJ
https://www.readbyqxmd.com/read/28430949/capturing-non-local-interactions-by-long-short-term-memory-bidirectional-recurrent-neural-networks-for-improving-prediction-of-protein-secondary-structure-backbone-angles-contact-numbers-and-solvent-accessibility
#6
Rhys Heffernan, Yuedong Yang, Kuldip Paliwal, Yaoqi Zhou
Motivation: The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some "short to intermediate" non-local interactions...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28403479/the-gard-platform-for-potency-assessment-of-skin-sensitizing-chemicals
#7
Kathrin S Zeller, Andy Forreryd, Tim Lindberg, Robin Gradin, Aakash Chawade, Malin Lindstedt
Contact allergy induced by certain chemicals is a common health concern, and several alternative methods have been developed to fulfill the requirements of European legislation with regard to hazard assessment of potential skin sensitizers. However, validated methods, which provide information about the potency of skin sensitizers, are still lacking. The cell-based assay Genomic Allergen Rapid Detection (GARD), targeting key event 3, dendritic cell activation, of the skin sensitizer AOP, uses gene expression profiling and a machine learning approach for the prediction of chemicals as sensitizers or non-sensitizers...
April 12, 2017: ALTEX
https://www.readbyqxmd.com/read/28383913/an-ensemble-based-protocol-for-the-computational-prediction-of-helix-helix-interactions-in-g-protein-coupled-receptors-using-coarse-grained-molecular-dynamics
#8
Nojood A Altwaijry, Michael Baron, David W Wright, Peter Vivian Coveney, Andrea Townsend-Nicholson
The accurate identification of the specific points of interaction between G protein-coupled receptor (GPCR) oligomers is essential for the design of receptor ligands targeting oligomeric receptor targets. A coarse-grained molecular dynamics computer simulation approach would provide a compelling means of identifying these specific protein-protein interactions and could be applied both for known oligomers of interest and as a high-throughput screen to identify novel oligomeric targets. However, to be effective, this in silico modeling must provide accurate, precise, and reproducible information...
April 6, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28383276/predicting-the-initial-steps-of-salt-stable-cowpea-chlorotic-mottle-virus-capsid-assembly-with-atomistic-force-fields
#9
Zoltan Antal, Janos Szoverfi, Szilard N Fejer
Computational prediction of native protein-protein interfaces still remains a challenging task. In virus capsids, each protein unit is in contact with copies of itself through several interfaces. The relative strengths of the different contacts affect the dynamics of the assembly, especially if the process is hierarchical. We investigate the dimerization of the salt-stable cowpea chlorotic mottle virus (CCMV) capsid protein using a combination of different computational tools. The best predictions of dimer configurations provided by blind docking with ZDOCK are rescored using geometry optimization with the Amber and Rosetta force fields...
April 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28383141/the-use-of-human-umbilical-vein-endothelial-cells-huvecs-as-an-in-vitro-model-to-assess-the-toxicity-of-nanoparticles-to-endothelium-a-review
#10
REVIEW
Yi Cao, Yu Gong, Liangliang Liu, Yiwei Zhou, Xin Fang, Cao Zhang, Yining Li, Juan Li
With the rapid development of nanotechnologies, nanoparticles (NPs) are increasingly produced and used in many commercial products, which could lead to the contact of human blood vessels with NPs. Thus, it is necessary to understand the adverse effects of NPs to relevant cells lining human blood vessels, especially endothelial cells (ECs) that cover the lumen of blood vessels. Human umbilical vein endothelial cells (HUVECs) are among one of the most popular models used for ECs in vitro. In the present review, we discussed studies that have used HUVECs as a model to investigate the EC-NP interactions, the toxic effects of NPs on ECs and the mechanisms...
April 6, 2017: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/28378120/comprehensive-analysis-of-the-in-vitro-and-ex-ovo-hemocompatibility-of-surface-engineered-iron-oxide-nanoparticles-for-biomedical-applications
#11
Florian Schlenk, Sebastian Werner, Martin Rabel, Franziska Jacobs, Christian Bergemann, Joachim H Clement, Dagmar Fischer
A set of biomedically relevant iron oxide nanoparticles with systematically modified polymer surfaces was investigated regarding their interaction with the first contact partners after systemic administration such as blood cells, blood proteins, and the endothelial blood vessels, to establish structure-activity relationships. All nanoparticles were intensively characterized regarding their physicochemical parameters. Cyto- and hemocompatibility tests showed that (1) the properties of the core material itself were not relevant in short-term incubation studies, and (2) toxicities increased with higher polymer mass, neutral = anionic < cationic surface charge and charge density, as well as agglomeration...
April 4, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28369334/nebcon-protein-contact-map-prediction-using-neural-network-training-coupled-with-na%C3%A3-ve-bayes-classifiers
#12
Baoji He, S M Mortuza, Yanting Wang, Hong-Bin Shen, Yang Zhang
Motivation: Recent CASP experiments have witnessed exciting progress on folding large-size non-humongous proteins with the assistance of co-evolution based contact predictions. The success is however anecdotal due to the requirement of the contact prediction methods for the high volume of sequence homologs that are not available to most of the non-humongous protein targets. Development of efficient methods that can generate balanced and reliable contact maps for different type of protein targets is essential to enhance the success rate of the ab initio protein structure prediction...
March 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28369168/conkit-a-python-interface-to-contact-predictions
#13
Felix Simkovic, Jens M H Thomas, Daniel J Rigden
Summary: Recent advances in protein residue contact prediction algorithms have led to the emergence of many new methods and a variety of file formats. We present ConKit , an open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions. Availability and implementation: ConKit is available via the Python Package Index. The documentation can be found at http://www...
March 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28369116/computational-prediction-of-the-tolerance-to-amino-acid-deletion-in-green-fluorescent-protein
#14
Eleisha L Jackson, Stephanie J Spielman, Claus O Wilke
Proteins evolve through two primary mechanisms: substitution, where mutations alter a protein's amino-acid sequence, and insertions and deletions (indels), where amino acids are either added to or removed from the sequence. Protein structure has been shown to influence the rate at which substitutions accumulate across sites in proteins, but whether structure similarly constrains the occurrence of indels has not been rigorously studied. Here, we investigate the extent to which structural properties known to covary with protein evolutionary rates might also predict protein tolerance to indels...
2017: PloS One
https://www.readbyqxmd.com/read/28363149/chemical-principles-additive-model-aligns-low-consensus-dna-targets-of-p53-tumor-suppressor-protein
#15
Kelly M Thayer, In Sub M Han
Computational prediction of the interaction between protein transcription factors and their cognate DNA binding sites in genomic promoters constitutes a formidable challenge in two situations: when the number of discriminatory interactions is small compared to the length of the binding site, and when DNA binding sites possess a poorly conserved consensus binding motif. The transcription factor p53 tumor suppressor protein and its target DNA exhibit both of these issues. From crystal structure analysis, only three discriminatory amino acid side chains contact the DNA for a binding site spanning ten base pairs...
March 22, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28348084/delineating-distinct-heme-scavenging-and-binding-functions-of-domains-in-mf6p-hdm-proteins-from-parasitic-flatworms
#16
Victoria Martínez-Sernández, Mercedes Mezo, Marta González-Warleta, María J Perteguer, Teresa Gárate, Fernanda Romarís, Florencio M Ubeira
MF6p/FhHDM-1 is a small protein secreted by the parasitic flatworm (trematode) Fasciola hepatica and belonging to a broad family of heme-binding proteins (MF6p/HDMs). MF6p/HDMs are of interest for understanding heme homeostasis in trematodes and also as potential targets for the development of new flukicides. Moreover, interest in these molecules has also increased due to their immunomodulatory properties. Here we have extended our previous findings on the mechanism of MF6p/HDM-heme interactions and have mapped the protein regions required for heme binding and for other biological functions...
March 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28338016/superposition-free-comparison-and-clustering-of-antibody-binding-sites-implications-for-the-prediction-of-the-nature-of-their-antigen
#17
Lorenzo Di Rienzo, Edoardo Milanetti, Rosalba Lepore, Pier Paolo Olimpieri, Anna Tramontano
We describe here a superposition free method for comparing the surfaces of antibody binding sites based on the Zernike moments and show that they can be used to quickly compare and cluster sets of antibodies. The clusters provide information about the nature of the bound antigen that, when combined with a method for predicting the number of direct antibody antigen contacts, allows the discrimination between protein and non-protein binding antibodies with an accuracy of 76%. This is of relevance in several aspects of antibody science, for example to select the framework to be used for a combinatorial antibody library...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337988/molecular-heterogeneity-in-major-urinary-proteins-of-mus-musculus-subspecies-potential-candidates-involved-in-speciation
#18
Jane L Hurst, Robert J Beynon, Stuart D Armstrong, Amanda J Davidson, Sarah A Roberts, Guadalupe Gómez-Baena, Carole M Smadja, Guila Ganem
When hybridisation carries a cost, natural selection is predicted to favour evolution of traits that allow assortative mating (reinforcement). Incipient speciation between the two European house mouse subspecies, Mus musculus domesticus and M.m.musculus, sharing a hybrid zone, provides an opportunity to understand evolution of assortative mating at a molecular level. Mouse urine odours allow subspecific mate discrimination, with assortative preferences evident in the hybrid zone but not in allopatry. Here we assess the potential of MUPs (major urinary proteins) as candidates for signal divergence by comparing MUP expression in urine samples from the Danish hybrid zone border (contact) and from allopatric populations...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28334762/missense-uros-mutations-causing-congenital-erythropoietic-porphyria-reduce-uros-homeostasis-that-can-be-rescued-by-proteasome-inhibition
#19
Jean-Marc Blouin, Ganeko Bernardo-Seisdedos, Emma Sasso, Julie Esteve, Cécile Ged, Magalie Lalanne, Arantza Sanz-Parra, Pedro Urquiza, Hubert de Verneuil, Oscar Millet, Emmanuel Richard
Congenital erythropoietic porphyria (CEP) is an inborn error of heme biosynthesis characterized by uroporphyrinogen III synthase (UROS) deficiency resulting in deleterious porphyrin accumulation in blood cells responsible for hemolytic anemia and cutaneous photosensitivity. We analyzed here the molecular basis of UROS impairment associated with twenty nine UROS missense mutations actually described in CEP patients. Using a computational and biophysical joint approach we predicted that most disease-causing mutations would affect UROS folding and stability...
April 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334219/a-network-model-predicts-the-intensity-of-residue-protein-thermal-coupling
#20
Luciano Censoni, Heloisa Dos Santos Muniz, Leandro Martínez
Motivation: The flow of vibrational energy in proteins has been shown not to obey expectations for isotropic media. The existence of preferential pathways for energy transport, with probable connections to allostery mechanisms, has been repeatedly demonstrated. Here, we investigate whether, by representing a set of protein structures as networks of interacting amino acid residues, we are able to model heat diffusion and predict residue-protein vibrational couplings, as measured by the Anisotropic Thermal Diffusion (ATD) computational protocol of modified molecular dynamics simulations...
March 7, 2017: Bioinformatics
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