review article | Q7318358 |
scholarly article | Q13442814 |
P50 | author | Kenno Vanommeslaeghe | Q38318385 |
Alex MacKerell | Q57907659 | ||
P2093 | author name string | Xi Cheng | |
Wei Han | |||
Benoît Roux | |||
Sunhwan Jo | |||
Wonpil Im | |||
Yifei Qi | |||
Lei Huang | |||
Hui Sun Lee | |||
Huan Rui | |||
Shahidul M Islam | |||
Allen Zhu | |||
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Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF | Q27646943 | ||
Structural determinants of nitroxide motion in spin-labeled proteins: Solvent-exposed sites in helix B of T4 lysozyme | Q27649381 | ||
Structural origin of weakly ordered nitroxide motion in spin-labeled proteins | Q27655050 | ||
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Recovery from slow inactivation in K+ channels is controlled by water molecules | Q37237569 | ||
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Chemoselective ligation and modification strategies for peptides and proteins. | Q37346260 | ||
Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations | Q37391160 | ||
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Dynamics transitions at the outer vestibule of the KcsA potassium channel during gating. | Q37571365 | ||
Unnatural amino acids as probes of ligand-receptor interactions and their conformational consequences. | Q38072101 | ||
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Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors | Q39597289 | ||
Molecular basis of NMDA receptor-coupled ion channel modulation by S-nitrosylation | Q40910444 | ||
Watching proteins move using site-directed spin labeling | Q40933370 | ||
All-atom polarizable force field for DNA based on the classical Drude oscillator model | Q41512422 | ||
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Contributions of counter-charge in a potassium channel voltage-sensor domain. | Q42023842 | ||
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Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. | Q42226830 | ||
Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds | Q42603831 | ||
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Reactivity of small thiolate anions and cysteine-25 in papain toward methyl methanethiosulfonate | Q43487689 | ||
DEER distance measurements on proteins | Q43666647 | ||
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The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations. | Q52210321 | ||
LAMBADA and InflateGRO2: efficient membrane alignment and insertion of membrane proteins for molecular dynamics simulations. | Q54327591 | ||
A novel reversible thiol-specific spin label: Papain active site labeling and inhibition | Q72928315 | ||
External cysteine residues in the serotonin transporter | Q73139649 | ||
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An expanded eukaryotic genetic code | Q28201981 | ||
Adding new chemistries to the genetic code | Q28277278 | ||
The art and practice of structure-based drug design: A molecular modeling perspective | Q29029768 | ||
Development and testing of a general amber force field | Q29547642 | ||
Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types | Q29616710 | ||
Automatic atom type and bond type perception in molecular mechanical calculations | Q29616744 | ||
Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores | Q30155430 | ||
Crystal structures of spin labeled T4 lysozyme mutants: implications for the interpretation of EPR spectra in terms of structure. | Q30327038 | ||
CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems. | Q30352184 | ||
Force Field for Peptides and Proteins based on the Classical Drude Oscillator | Q30358273 | ||
A general method for site-specific incorporation of unnatural amino acids into proteins. | Q30380652 | ||
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Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins | Q30405636 | ||
Three-dimensional architecture and gating mechanism of a K+ channel studied by EPR spectroscopy | Q30472195 | ||
Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme | Q30603705 | ||
Automated builder and database of protein/membrane complexes for molecular dynamics simulations | Q33298604 | ||
Simulations of the role of water in the protein-folding mechanism | Q33694936 | ||
Conformational dynamics of ligand-dependent alternating access in LeuT. | Q33729757 | ||
Additive empirical force field for hexopyranose monosaccharides | Q33899141 | ||
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Biomolecular simulation: a computational microscope for molecular biology | Q34266180 | ||
Empirical force fields for biological macromolecules: overview and issues. | Q34334583 | ||
The GROMOS software for biomolecular simulation: GROMOS05. | Q34457783 | ||
Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes | Q34537730 | ||
Design of functional metalloproteins | Q34659023 | ||
AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA | Q35040558 | ||
Structure and dynamics of a conformationally constrained nitroxide side chain and applications in EPR spectroscopy | Q35239853 | ||
Activation pathway of Src kinase reveals intermediate states as targets for drug design | Q35738216 | ||
How does voltage open an ion channel? | Q36480474 | ||
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles | Q36546184 | ||
CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application | Q36569443 | ||
Cysteine substitution mutagenesis and the effects of methanethiosulfonate reagents at P2X2 and P2X4 receptors support a core common mode of ATP action at P2X receptors. | Q36761837 | ||
Mechanism for alternating access in neurotransmitter transporters | Q36785076 | ||
Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy | Q36933157 | ||
CHARMMing: a new, flexible web portal for CHARMM. | Q37176721 | ||
P921 | main subject | CHARMM | Q902642 |
P304 | page(s) | 235-265 | |
P577 | publication date | 2014-08-24 | |
P1433 | published in | Advances in protein chemistry and structural biology | Q26841838 |
P1476 | title | CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues | |
P478 | volume | 96 |
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Q49935761 | From a highly-disordered to a metastable state: Uncovering insights of α-synuclein. |
Q33459363 | Glycan Reader is Improved to Recognize Most Sugar Types and Chemical Modifications in the Protein Data Bank. |
Q38644272 | Identification of two natural compound inhibitors of Leishmania donovani Spermidine Synthase (SpdS) through molecular docking and dynamic studies |
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Q47191286 | Relationship between lignocellulosic biomass dissolution and physicochemical properties of ionic liquids composed of 3-methylimidazolium cations and carboxylate anions |
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