Protein structure determination using PCSs and Rosetta
Protein 3D structure determination using homology modeling and structure analysis
... 1 Department of Biotechnology, 2 Department of Zoology, Mizoram University, Aizawl 796 004, India 3 Department of Information Technology, ICFAI University, Aizawl, India A BSTRACT The protein sequence of aspartate ...
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Rapid Calculation of Protein pKa Values Using Rosetta
... further calculations in structure prediction and design. Rosetta’s physics-based all-atom energy function (with terms for van der Waals, solvation, hydrogen bonding, etc.) is pairwise-additive and has used ...
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A Method for Integrative Structure Determination of Protein- Protein Complexes
... with protein flexibility and the absence of an accurate scoring function (Ritchie, ...Pairwise protein docking methods can be divided into three classes based on their configurational sampling algorithm ...
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Calculation of Membrane Protein Structures in Oriented-Sample NMR and Their Validation Using Rosetta.
... native structure, so the lowest energy obtained with this OCTOPUS topology file (around -20) is also about half of the lowest energy of the model close to the native structure (around ...the Rosetta ...
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Structure Determination of Protein-Protein Complexes Using NMR Chemical Shifts: Case of an Endonuclease Colicin-Immunity Protein Complex
... The great majority of cellular processes, such as enzyme catalysis, signal transduction, gene expression regulation, and the immune response, depend on the formation of transient or permanent macromolecular complexes. ...
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Membrane protein structure determination using crystallography and lipidic mesophases: recent advances and successes
... hetero-trimeric protein with 23 transmembrane helices and a cytochrome c-like domain as a C-terminal extension to one of its ...produce structure-grade ...a structure of a protein, LHII, whose ...
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Geometric Algorithms for Protein Structure Determination Using Measurements From Nuclear Magnetic Resonance Spectroscopy
... High-resolution structure determination of homo-oligomeric protein complexes remains a daunting task for NMR ...and determination of the structure of each subunit within the oligomeric ...
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Optimizing an Emperical Scoring Function for Transmembrane Protein Structure Determination
... transmembrane protein structure determination process proposed in [17, ...Moreover, using local optimization methods is not a disadvantage on such a ...
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Experimental phasing for structure determination using membrane protein crystals grown by the lipid cubic phase method
... membrane- protein structures solved using crystals grown by the lipid cubic phase or in meso method, only ten have been determined by ...meso structure of the integral membrane diacylglycerol kinase ...
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Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS
... The present validation of NOESY peak picking and NOE cross peak identification by ATNOS is based on using the resulting peak lists as input for automated NOE assignment with CANDID (Herr[r] ...
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Single particle 2D Electron crystallography for membrane protein structure determination
... requirements, using the meta-compression library ...compression using the zStandard codec, file input-output rates are accelerated and archival storage requirements are ...
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Development of nuclear magnetic resonance methods for determination of membrane protein structure
... probed. Using isotopically labelled leucine and phenylalanine a BPV E5 LF ssNMR sample was prepared in a similar manner to singly labelled ...GpA. Using 1D 13 C analysis of BPV E5 in DMPC/cholesterol ...
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New methods for automated NMD data analysis and protein structure determination
... out using the substrate bound form of the Sud protein shows a positively charged binding pocket that covers partially the polysulfide ligand, which explains the uneven distribution of the dissociation ...
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Fragon: rapid high-resolution structure determination from ideal protein fragments
... ideal protein fragments by molecular replacement presents an attractive method for obtaining preliminary phases when no template structure for molecular replacement is ...placed using Phaser and the ...
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Requirements on Paramagnetic Relaxation Enhancement Data for Membrane Protein Structure Determination by NMR
... the structure determination of a-helical membrane proteins ( Table ...the structure calculations with our PRE-based data ...labels. Using RDCs improved the backbone rmsd values to the ...
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Modern Methods of Protein Crystal Structure Determination and Structural Analysis of RNA Polymerase
... X-ray protein structure analysis methods are relatively new and fast developing tools for determination of structure of organic ...a protein or nucleic acid structure at atomic ...
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Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination
... If using high-throughput techniques, including ligase independent cloning, combined with small scale expression and solubilization tests the answer may very well be ...
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An investigation of three-finger toxin – nAChR interactions through Rosetta protein docking
... of using the native protein structures for the re-docking calculations is imprinting structural information that bias the docking ...of protein structures with different ligands bound in their native ...
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Determination of protein structural ensembles using cryo-electron microscopy.
... A representative example of the opportunities offered by integrative approaches is the recent characterization of the structure and dynamics of the ClpP protease by a combined cryo-EM and NMR strategy [68]. In ...
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Crystallizing membrane proteins for structure determination using lipidic mesophases
... membrane protein whose structure was determined using ...the protein is required to do ...in structure determination using macromolecular ...membrane protein ...
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