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https://www.readbyqxmd.com/read/28066917/balancing-exploration-and-exploitation-in-population-based-sampling-improves-fragment-based-de-novo-protein-structure-prediction
#1
David Simoncini, Thomas Schiex, Kam Y J Zhang
Conformational search space exploration remains a major bottleneck for protein structure prediction methods. Population-based meta-heuristics typically enable the possibility to control the search dynamics and to tune the balance between local energy minimization and search space exploration. EdaFold is a fragment-based approach that can guide search by periodically updating the probability distribution over the fragment libraries used during model assembly. We implement the EdaFold algorithm as a Rosetta protocol and provide two different probability update policies: a cluster-based variation (EdaRosec ) and an energy-based one (EdaRoseen ) We analyze the search dynamics of our new Rosetta protocols and show that EdaRosec EdaRosec is able to provide predictions with lower Cα RMSD to the native structure than EdaRoseen and Rosetta AbInitio Relax protocol...
January 9, 2017: Proteins
https://www.readbyqxmd.com/read/28058667/evaluation-of-high-risk-features-of-primary-enucleation-of-patients-with-retinoblastoma-in-a-tertiary-center-of-a-developing-country-in-the-era-of-intra-arterial-chemotherapy
#2
Funda Dikkaya, Ahmet Murat Sarıcı, Firuze Erbek, Tiraje Celkan, Mehmet Serhat Mangan, Övgü Aydın, Cuyan Demirkesen, Halit Pazarlı
PURPOSE: To evaluate the frequency of high-risk histopathologic factors in Turkish children enucleated for retinoblastoma and to analyze the association between growth pattern, rosetta formation, tumor thickness, presence of necrosis, calcification, neovascularization, rate of mitosis, and high-risk histopathologic factors. METHODS: Pathology reports of 59 eyes who had received enucleation for retinoblastoma were reviewed retrospectively. The histopathologic data included presence of choroidal invasion, optic nerve invasion, scleral extension, tumor thickness, presence of necrosis, calcification, neovascularization, rosetta formation and lymphocyte infiltration, rate of mitosis, and growth pattern...
January 5, 2017: International Ophthalmology
https://www.readbyqxmd.com/read/28052191/engineering-a-thermostable-keto-acid-decarboxylase-using-directed-evolution-and-computationally-directed-protein-design
#3
Lemuel M J Soh, Wai Shun Mak, Paul P Lin, Luo Mi, Frederic Y-H Chen, Robert Damoiseaux, Justin B Siegel, James C Liao
Keto acid decarboxylase (Kdc) is a key enzyme in producing keto acid derived higher alcohols, like isobutanol. The most active Kdc's are found in mesophiles; the only reported Kdc activity in thermophiles is 2 orders of magnitude less active. Therefore, the thermostability of mesophilic Kdc limits isobutanol production temperature. Here, we report development of a thermostable 2-ketoisovalerate decarboxylase (Kivd) with 10.5-fold increased residual activity after 1h preincubation at 60 °C. Starting with mesophilic Lactococcus lactis Kivd, a library was generated using random mutagenesis and approximately 8,000 independent variants were screened...
January 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28045385/crystal-structure-of-human-chondroadherin-solving-a-difficult-molecular-replacement-problem-using-de-novo-models
#4
Sebastian Rämisch, Anna Pramhed, Viveka Tillgren, Anders Aspberg, Derek T Logan
Chondroadherin (CHAD) is a cartilage matrix protein that mediates the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats (LRR) flanked by cysteine-rich domains. CHAD makes important interactions with collagen as well as with cell-surface heparin sulfate proteoglycans and α2β1 integrins. The integrin-binding site is located in a region of hitherto unknown structure at the C-terminal end of CHAD. Peptides based on the C-terminal human CHAD (hCHAD) sequence have shown therapeutic potential for treating osteoporosis...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28011777/expanding-the-toolkit-for-membrane-protein-modeling-in-rosetta
#5
Julia Koehler Leman, Benjamin K Mueller, Jeffrey J Gray
MOTIVATION: A range of membrane protein modeling tools has been developed in the past 5-10 years, yet few of these tools are integrated and make use of existing functionality for soluble proteins. To extend existing methods in the Rosetta biomolecular modeling suite for membrane proteins, we recently implemented RosettaMP, a general framework for membrane protein modeling. While RosettaMP facilitates implementation of new methods, addressing real-world biological problems also requires a set of accessory tools that are used to carry out standard modeling tasks...
December 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28008041/rosetta-observes-sublimating-surface-ices
#6
EDITORIAL
Keith T Smith
No abstract text is available yet for this article.
December 23, 2016: Science
https://www.readbyqxmd.com/read/28002624/flexpepdock-lessons-from-capri-peptide-protein-rounds-and-suggested-new-criteria-for-assessment-of-model-quality-and-utility
#7
Orly Marcu, Emma-Joy Dodson, Nawsad Alam, Michal Sperber, Dima Kozakov, Marc F Lensink, Ora Schueler-Furman
CAPRI rounds 28 and 29 included, for the first time, peptide-receptor targets of three different systems, reflecting increased appreciation of the importance of peptide-protein interactions. The CAPRI rounds allowed us to objectively assess the performance of Rosetta FlexPepDock, one of the first protocols to explicitly include peptide flexibility in docking, accounting for peptide conformational changes upon binding. We discuss here successes and challenges in modeling these targets: we obtain top-performing, high-resolution models of the peptide motif for cases with known binding sites but there is a need for better modeling of flanking regions, as well as better selection criteria, in particular for unknown binding sites...
December 21, 2016: Proteins
https://www.readbyqxmd.com/read/27993124/reduced-fragment-diversity-for-alpha-and-alpha-beta-protein-structure-prediction-using-rosetta
#8
Jad Abbass, Jean-Christophe Nebel
Protein structure prediction is still considered a main challenge in computational biology. The biannual international competition, Critical Assessment of protein Structure Prediction (CASP), has shown in its eleventh version that free modelling targets' predictions are still beyond reliable accuracy, therefore, much efforts should be done for ab initio methods. Arguably, Rosetta is considered as the most competitive method when it comes to targets with no homologues. Relying on fragments of length 9 and 3 from known structures, Rosetta creates putative structures by assembling candidate fragments...
December 16, 2016: Protein and Peptide Letters
https://www.readbyqxmd.com/read/27988855/assessment-of-the-fusion-tags-on-increasing-soluble-production-of-the-active-tev-protease-variant-and-other-target-proteins-in-e-coli
#9
Xuelian Yu, Jiaqi Sun, Weiyu Wang, Li Jiang, Beijiu Cheng, Jun Fan
In this study, five fusion tags affecting soluble production and cleavage activity of the tobacco etch virus (TEV) protease (TEVp) variant in Escherichia coli strains BL21 (DE3) and Rosetta™ (DE3) are investigated. Combination of the augmenting rare transfer RNAs (tRNAs) and the fused expressivity tag (N-terminal seven amino acid residues of E. coli translation initiation factor II) promotes the soluble TEVp partner expressed at relatively high level. Attachment of the maltose-binding protein (MBP) tag increases soluble expression of the protease released from the fusion protein in E...
December 17, 2016: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/27974464/affinity-maturation-of-a-cyclic-peptide-handle-for-therapeutic-antibodies-using-deep-mutational-scanning
#10
Martijn van Rosmalen, Brian M G Janssen, Nathalie M Hendrikse, Ardjan J van der Linden, Pascal A Pieters, Dave Wanders, Tom F A de Greef, Maarten Merkx
Meditopes are cyclic peptides that bind in a specific pocket in the antigen-binding fragment (Fab) of a therapeutic antibody such as cetuximab. Provided their moderate affinity can be enhanced, meditope peptides could be used as a specific non-covalent and paratope-independent handles in targeted drug delivery, molecular imaging and therapeutic drug monitoring. Here we show that the affinity of a recently reported meditope for cetuximab can be substantially enhanced using a combination of yeast display and deep mutational scanning...
December 14, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27967109/filter-feeding-near-field-flows-and-the-morphologies-of-colonial-choanoflagellates
#11
Julius B Kirkegaard, Raymond E Goldstein
Efficient uptake of prey and nutrients from the environment is an important component in the fitness of all microorganisms, and its dependence on size may reveal clues to the origins of evolutionary transitions to multicellularity. Because potential benefits in uptake rates must be viewed in the context of other costs and benefits of size, such as varying predation rates and the increased metabolic costs associated with larger and more complex body plans, the uptake rate itself is not necessarily that which is optimized by evolution...
November 2016: Physical Review. E
https://www.readbyqxmd.com/read/27940918/computational-design-of-a-homotrimeric-metalloprotein-with-a-trisbipyridyl-core
#12
Jeremy H Mills, William Sheffler, Maraia E Ener, Patrick J Almhjell, Gustav Oberdorfer, José Henrique Pereira, Fabio Parmeggiani, Banumathi Sankaran, Peter H Zwart, David Baker
Metal-chelating heteroaryl small molecules have found widespread use as building blocks for coordination-driven, self-assembling nanostructures. The metal-chelating noncanonical amino acid (2,2'-bipyridin-5yl)alanine (Bpy-ala) could, in principle, be used to nucleate specific metalloprotein assemblies if introduced into proteins such that one assembly had much lower free energy than all alternatives. Here we describe the use of the Rosetta computational methodology to design a self-assembling homotrimeric protein with [Fe(Bpy-ala)3](2+) complexes at the interface between monomers...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27936510/systematic-evaluation-of-cs-rosetta-for-membrane-protein-structure-prediction-with-sparse-noe-restraints
#13
Katrin Reichel, Olivier Fisette, Tatjana Braun, Olivier F Lange, Gerhard Hummer, Lars V Schäfer
We critically test and validate the CS-Rosetta methodology for de novo structure prediction of α-helical membrane proteins (MPs) from NMR data, such as chemical shifts and NOE distance restraints. By systematically reducing the number and type of NOE restraints, we focus on determining the regime in which MP structures can be reliably predicted and pinpoint the boundaries of the approach. Five MPs of known structure were used as test systems, phototaxis sensory rhodopsin II (pSRII), a subdomain of pSRII, disul_de binding protein B (DsbB), microsomal prostaglandin E2 synthase-1 (mPGES-1), and translocator protein (TSPO)...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27932294/large-scale-structure-based-prediction-and-identification-of-novel-protease-substrates-using-computational-protein-design
#14
Manasi A Pethe, Aliza B Rubenstein, Sagar D Khare
Characterizing the substrate specificity of protease enzymes is critical for illuminating the molecular basis of their diverse and complex roles in a wide array of biological processes. Rapid and accurate prediction of their extended substrate specificity would also aid in the design of custom proteases capable of selectively and controllably cleaving biotechnologically or therapeutically relevant targets. However, current in silico approaches for protease specificity prediction, rely on, and are therefore limited by, machine learning of sequence patterns in known experimental data...
December 6, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27918427/prolactin-friend-or-foe-in-central-nervous-system-autoimmune-inflammation
#15
REVIEW
Massimo Costanza, Rosetta Pedotti
The higher prevalence of multiple sclerosis (MS) in females, along with the modulation of disease activity observed during pregnancy and the post-partum period, has suggested a hormonal influence in MS. Even if prolactin (PRL) does not belong to the sex hormones family, its crucial role in female reproduction and lactation has prompted great efforts to understand if PRL could represent a gender factor in the pathogenesis of MS and experimental autoimmune encephalomyelitis (EAE), the animal model for this disease...
December 2, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27916743/clipping-of-the-tricuspid-valve-proposal-of-a-rosetta-stone-nomenclature-for-procedural-3d-transesophageal-guidance
#16
Maurizio Taramasso, Michel Zuber, Fabian Nietlispach, Francesco Maisano
No abstract text is available yet for this article.
December 6, 2016: EuroIntervention
https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#17
Christine E Tinberg, Sagar D Khare
The ability to design novel small-molecule binding sites in proteins is a stringent test of our understanding of the principles of molecular recognition, and would have many practical applications, in synthetic biology and medicine. Here, we describe a computational method in the context of the macromolecular modeling suite Rosetta to designing proteins with sites featuring predetermined interactions to ligands of choice. The required inputs for the method are a model of the small molecule and the desired interactions (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27908283/expression-of-a-fungal-manganese-peroxidase-in-escherichia-coli-a-comparison-between-the-soluble-and-refolded-enzymes
#18
Nan Wang, Kai Ren, Rong Jia, Wenting Chen, Ruirui Sun
BACKGROUND: Manganese peroxidase (MnP) from Irpex lacteus F17 has been shown to have a strong ability to degrade recalcitrant aromatic pollutants. In this study, a recombinant MnP from I. lacteus F17 was expressed in Escherichia coli Rosetta (DE3) in the form of inclusion bodies, which were refolded to achieve an active enzyme. Further, we optimized the in vitro refolding conditions to increase the recovery yield of the recombinant protein production. Additionally, we attempted to express recombinant MnP in soluble form in E...
December 1, 2016: BMC Biotechnology
https://www.readbyqxmd.com/read/27900782/residue-centric-modeling-and-design-of-saccharide-and-glycoconjugate-structures
#19
Jason W Labonte, Jared Adolf-Bryfogle, William R Schief, Jeffrey J Gray
The RosettaCarbohydrate framework is a new tool for modeling a wide variety of saccharide and glycoconjugate structures. This report describes the development of the framework and highlights its applications. The framework integrates with established protocols within the Rosetta modeling and design suite, and it handles the vast complexity and variety of carbohydrate molecules, including branching and sugar modifications. To address challenges of sampling and scoring, RosettaCarbohydrate can sample glycosidic bonds, side-chain conformations, and ring forms, and it utilizes a glycan-specific term within its scoring function...
February 15, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/27890597/identification-eukaryotic-expression-and-structure-function-characterizations-of-%C3%AE-defensin-like-homologues-from-pelodiscus-sinensis
#20
Haining Yu, Hui Wang, Xuelian Liu, Lan Feng, Xue Qiao, Shasha Cai, Nannan Shi, Yipeng Wang
Defensins are a group of host defense peptides that play a central role in host innate immune responses. Here, 26 genes encoding β-defensin-like peptides have been identified for the first time in Pelodiscus sinensis using database mining approach. Phylogenetic study confirmed that β-defensins are fast evolving genes with high rates of sequence substitutions. The expression level of several selected genes in different tissues was examined by RT-PCR. Ps-BDs mainly adopt β-strands and/or α-helix conformations homology modeled by Rosetta program...
March 2017: Developmental and Comparative Immunology
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