CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. (Q36539936)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25443960%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

review article

1 reference

title

CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues (English)

1 reference

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23 February 2020

1 reference

1 reference

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23 February 2020

1 reference

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23 February 2020

Sunhwan Jo

1 reference

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23 February 2020

Xi Cheng

1 reference

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23 February 2020

Shahidul M Islam

1 reference

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23 February 2020

Lei Huang

1 reference

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23 February 2020

Huan Rui

1 reference

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23 February 2020

Allen Zhu

1 reference

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23 February 2020

Hui Sun Lee

1 reference

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23 February 2020

Yifei Qi

1 reference

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23 February 2020

Wei Han

1 reference

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23 February 2020

Benoît Roux

1 reference

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23 February 2020

Wonpil Im

1 reference

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23 February 2020

publication date

24 August 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25443960%20AND%20SRC:MED&resulttype=core&format=json

Advances in protein chemistry and structural biology

23 February 2020

published in

1 reference

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23 February 2020

volume

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23 February 2020

page(s)

235-265

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25443960%20AND%20SRC:MED&resulttype=core&format=json

Conformational dynamics of ligand-dependent alternating access in LeuT.

23 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Activation pathway of Src kinase reveals intermediate states as targets for drug design

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Force Field for Peptides and Proteins based on the Classical Drude Oscillator

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Dynamics transitions at the outer vestibule of the KcsA potassium channel during gating.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Rapid parameterization of small molecules using the Force Field Toolkit

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Recovery from slow inactivation in K+ channels is controlled by water molecules

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Unnatural amino acids as probes of ligand-receptor interactions and their conformational consequences.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Biomolecular simulation: a computational microscope for molecular biology

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

MATCH: an atom-typing toolset for molecular mechanics force fields.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Open Babel: An open chemical toolbox

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Structure and dynamics of a conformationally constrained nitroxide side chain and applications in EPR spectroscopy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

SwissParam: A fast force field generation tool for small organic molecules

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

The RCSB Protein Data Bank: redesigned web site and web services

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

WIWS: a protein structure bioinformatics Web service collection

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Adding new chemistries to the genetic code

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Design of functional metalloproteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

CHARMM: the biomolecular simulation program

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Structural origin of weakly ordered nitroxide motion in spin-labeled proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Chemoselective ligation and modification strategies for peptides and proteins.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

CHARMMing: a new, flexible web portal for CHARMM.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Mechanism for alternating access in neurotransmitter transporters

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

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.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Additive empirical force field for hexopyranose monosaccharides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Structural determinants of nitroxide motion in spin-labeled proteins: Solvent-exposed sites in helix B of T4 lysozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Automated builder and database of protein/membrane complexes for molecular dynamics simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Structural determinants of nitroxide motion in spin-labeled proteins: Tertiary contact and solvent-inaccessible sites in helix G of T4 lysozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

How does voltage open an ion channel?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Automatic atom type and bond type perception in molecular mechanical calculations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

The GROMOS software for biomolecular simulation: GROMOS05.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Empirical force fields for biological macromolecules: overview and issues.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Development and testing of a general amber force field

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Simulations of the role of water in the protein-folding mechanism

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

An expanded eukaryotic genetic code

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Crystal structures of spin labeled T4 lysozyme mutants: implications for the interpretation of EPR spectra in terms of structure.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Molecular basis of NMDA receptor-coupled ion channel modulation by S-nitrosylation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Three-dimensional architecture and gating mechanism of a K+ channel studied by EPR spectroscopy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Watching proteins move using site-directed spin labeling

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

The art and practice of structure-based drug design: A molecular modeling perspective

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

A general method for site-specific incorporation of unnatural amino acids into proteins.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

All-atom polarizable force field for DNA based on the classical Drude oscillator model

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

LIPID11: a modular framework for lipid simulations using amber

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Contributions of counter-charge in a potassium channel voltage-sensor domain.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Motion of spin-labeled side chains in T4 lysozyme: effect of side chain structure

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Reactivity of small thiolate anions and cysteine-25 in papain toward methyl methanethiosulfonate

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

LAMBADA and InflateGRO2: efficient membrane alignment and insertion of membrane proteins for molecular dynamics simulations.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

DEER distance measurements on proteins

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

Energetics of ion conduction through the K+ channel

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739825

CHARMM-GUI: a web-based graphical user interface for CHARMM

21 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25443960

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A novel reversible thiol-specific spin label: Papain active site labeling and inhibition

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25443960

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

External cysteine residues in the serotonin transporter

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25443960

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/BS.APCSB.2014.06.002

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25443960%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25443960%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

PubMed publication ID

25443960

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25443960%20AND%20SRC:MED&resulttype=core&format=json