H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations - Test2 - elhamkhani - TriplyDB

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

http://www.wikidata.org/entity/Q36088442

about

Alternate splicing of dysferlin C2A confers Ca²⁺-dependent and Ca²⁺-independent binding for membrane repair A gating mechanism for Pi release governs the mRNA unwinding by eIF4AI during translation initiation.Induced opening of influenza virus neuraminidase N2 150-loop suggests an important role in inhibitor binding Structure of the epimerization domain of tyrocidine synthetase A Visualizing phosphodiester-bond hydrolysis by an endonuclease Directed divergent evolution of a thermostable D-tagatose epimerase towards improved activity for two hexose substrates Structure and reaction mechanism of a novel enone reductase Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution Structure of the F-actin-tropomyosin complex Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations Thermal adaptation of conformational dynamics in ribonuclease H Interaction between trehalose and MTHase from Sulfolobus solfataricus studied by theoretical computation and site-directed mutagenesis A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation How Intrinsic Molecular Dynamics Control Intramolecular Communication in Signal Transducers and Activators of Transcription Factor STAT5 Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase All-Atom Molecular Dynamics of Virus Capsids as Drug Targets Building a virtual ligand screening pipeline using free software: a survey Predictive approach for protein aggregation: Correlation of protein surface characteristics and conformational flexibility to protein aggregation propensity.Conformational flexibility related to enzyme activity: evidence for a dynamic active-site gatekeeper function of Tyr(215) in Aerococcus viridans lactate oxidase.Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation.Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways.Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin.The alteration of the C-terminal region of human frataxin distorts its structural dynamics and function.Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L (CbpL) Contributing to Pneumococcal Pathogenesis In search of tail-anchored protein machinery in plants: reevaluating the role of arsenite transporters.Two-step ATP-driven opening of cohesin head Different pH-dependencies of the two synaptic adhesion molecules N-cadherin and cadherin-11 and the possible functional implication for long-term potentiation.Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field Molecular Dynamics Study of Helicobacter pylori Urease.Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site.Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5.Recent development and application of constant pH molecular dynamics Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations A partition function approximation using elementary symmetric functions.VP40 of the Ebola Virus as a Target for EboV Therapy: Comprehensive Conformational and Inhibitor Binding Landscape from Accelerated Molecular Dynamics.New insights into the binding and catalytic mechanisms of Bacillus thuringiensis lactonase: insights into B. thuringiensis AiiA mechanism.Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies In silico insights into protein-protein interactions and folding dynamics of the saposin-like domain of Solanum tuberosum aspartic protease.

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P2860

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

http://www.wikidata.org/entity/Q36088442

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2012 nî lūn-bûn

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name

H++ 3.0: automating pK predict ...... cular modeling and simulations

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H++ 3.0: automating pK predict ...... cular modeling and simulations

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H++ 3.0: automating pK predict ...... cular modeling and simulations

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H++ 3.0: automating pK predict ...... cular modeling and simulations

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H++ 3.0: automating pK predict ...... cular modeling and simulations

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H++ 3.0: automating pK predict ...... cular modeling and simulations

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Nucleic Acids Research

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H++ 3.0: automating pK predict ...... cular modeling and simulations

@en

P2093

Alexey V Onufriev

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Boris Aguilar

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P2860

Open Babel: An open chemical toolbox

The Protein Data Bank

H++: a server for estimating pKas and adding missing hydrogens to macromolecules

A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein-water interface as a determinant of pKavalues

Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease

The Amber biomolecular simulation programs

Molecular dynamics and protein function.

A Novel View of pH Titration in Biomolecules†

Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

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W537-41

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scholarly article

P356

10.1093/NAR/GKS375

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Web Server issue

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P478

40

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Ramu Anandakrishnan

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2012-05-08T00:00:00Z

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224926310

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22570416

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3394296

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