GalaxyRefine: Protein structure refinement driven by side-chain repacking - Test2 - elhamkhani - TriplyDB

GalaxyRefine: Protein structure refinement driven by side-chain repacking

GalaxyRefine: Protein structure refinement driven by side-chain repacking

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Structural models of zebrafish (Danio rerio) NOD1 and NOD2 NACHT domains suggest differential ATP binding orientations: insights from computational modeling, docking and molecular dynamics simulations Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines.WeFold: a coopetition for protein structure prediction The origin of consistent protein structure refinement from structural averaging.Protein structure refinement via molecular-dynamics simulations: What works and what does not?CASP11--An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline.3Drefine: an interactive web server for efficient protein structure refinement.Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD.Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment.Molecular and Structural Characterization of the Tegumental 20.6-kDa Protein in Clonorchis sinensis as a Potential Druggable Target.GalaxySite: ligand-binding-site prediction by using molecular docking.Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif.SDRL: a sequence-dependent protein side-chain rotamer library.GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization.Rational design of DKK3 structure-based small peptides as antagonists of Wnt signaling pathway and in silico evaluation of their efficiency Galaxy7TM: flexible GPCR-ligand docking by structure refinement GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking.A novel homozygous mutation in the EC1/EC2 interaction domain of the gap junction complex connexon 26 leads to profound hearing impairment Structural and functional characterization of the α-catenin·β-catenin binding interface in Caenorhabditis elegans reveals conserved requirements for cell-cell adhesion in metazoans.Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection.Effective protein model structure refinement by loop modeling and overall relaxation.The Potato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor Rx1 Is a Pathogen-dependent DNA-deforming Protein.HBsAg mutations related to occult hepatitis B virus infection in HIV-positive patients result in a reduced secretion and conformational changes of HBsAg.Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds.Ribonucleotide Reductases from Bifidobacteria Contain Multiple Conserved Indels Distinguishing Them from All Other Organisms: In Silico Analysis of the Possible Role of a 43 aa Bifidobacteria-Specific Insert in the Class III RNR Homolog.Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motif.ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates.The Tomato Nucleotide-binding Leucine-rich Repeat Immune Receptor I-2 Couples DNA-binding to Nucleotide-binding Domain Nucleotide Exchange.Activation of the LRR Receptor-Like Kinase PSY1R Requires Transphosphorylation of Residues in the Activation Loop.Enhancing the Thermostability of Rhizomucor miehei Lipase with a Limited Screening Library by Rational-Design Point Mutations and Disulfide Bonds.PREFMD: a web server for protein structure refinement via molecular dynamics simulations.Novel Immunoinformatics Approaches to Design Multi-epitope Subunit Vaccine for Malaria by Investigating Anopheles Salivary Protein.Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment.Molecular dynamics insights into the structure, function, and substrate binding mechanism of mucin desulfating sulfatase of gut microbe Bacteroides fragilis.Molecular interactions between tubulin tails and glutamylases reveal determinants of glutamylation patterns.Anti-ROR1 scFv-EndoG as a Novel Anti-Cancer Therapeutic Drug Romo1 is a mitochondrial nonselective cation channel with viroporin-like characteristics.Identification of coding sequence and its use for functional and structural characterization of catalase from Phyllanthus emblica.Immune-Informatic Analysis and Design of Peptide Vaccine From Multi-epitopes Against Corynebacterium pseudotuberculosis.Assessment of ab initio models of protein complexes by molecular dynamics.

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P2860

GalaxyRefine: Protein structure refinement driven by side-chain repacking

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2013 nî lūn-bûn

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2013 թուականի Յունիսին հրատարակուած գիտական յօդուած

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2013 թվականի հունիսին հրատարակված գիտական հոդված

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2013年の論文

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2013年論文

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2013年論文

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2013年論文

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2013年論文

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2013年论文

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name

GalaxyRefine: Protein structure refinement driven by side-chain repacking

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GalaxyRefine: Protein structure refinement driven by side-chain repacking

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GalaxyRefine: Protein structure refinement driven by side-chain repacking

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Chaok Seok

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Hahnbeom Park

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Lim Heo

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The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models.

I-TASSER: a unified platform for automated protein structure and function prediction

Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling

MolProbity: all-atom structure validation for macromolecular crystallography

LGA: A method for finding 3D similarities in protein structures

All-atom empirical potential for molecular modeling and dynamics studies of proteins

Comparative protein structure modeling of genes and genomes

Rotamer libraries in the 21st century

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

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10.1093/NAR/GKT458

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Web Server issue

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41

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2013-06-03T00:00:00Z

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