(Q30053209)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

title

Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

Chris A. Kieslich

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

3

James Smadbeck

0 references

Christodoulos Floudas

series ordinal

5

object named as

Christodoulos A Floudas

0 references

author name string

Jeff P Thompson

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

publication date

1 December 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Theory and Computation

7 March 2020

published in

2 references

25 May 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

volume

9

2 references

25 May 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

issue

12

2 references

25 May 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

page(s)

5653-5674

2 references

25 May 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

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

7 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

ASTRO-FOLD 2.0: an Enhanced Framework for Protein Structure Prediction

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Toward convergence of experimental studies and theoretical modeling of the chromatin fiber

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Structural basis of substrate methylation and inhibition of SMYD2

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

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

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

The conserved glu in the cyclotide cycloviolacin O2 has a key structural role

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Computational design of Candida boidinii xylose reductase for altered cofactor specificity

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Dynamic and structural characterization of a bacterial FHA protein reveals a new autoinhibition mechanism

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Comparison of multiple Amber force fields and development of improved protein backbone parameters

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Conformational changes in protein loops and helices induced by post-translational phosphorylation

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Automatic atom type and bond type perception in molecular mechanical calculations

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

TM-align: a protein structure alignment algorithm based on the TM-score

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Development and testing of a general amber force field

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Exploring protein native states and large-scale conformational changes with a modified generalized born model

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

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

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Translating the Histone Code

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

26 May 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Areas, volumes, packing and protein structure

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Protein folding and de novo protein design for biotechnological applications

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Revised AMBER parameters for bioorganic phosphates

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

SwissSidechain: a molecular and structural database of non-natural sidechains

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Post-translational modifications induce significant yet not extreme changes to protein structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Allosteric post-translational modification codes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Refinement of protein structure homology models via long, all-atom molecular dynamics simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

De novo peptide design with C3a receptor agonist and antagonist activities: theoretical predictions and experimental validation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Template-based protein structure modeling using TASSER(VMT.).

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Discovery of entry inhibitors for HIV-1 via a new de novo protein design framework.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Post-translational modifications in signal integration

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

New compstatin variants through two de novo protein design frameworks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Importance of charge independent effects in readout of the trimethyllysine mark by HP1 chromodomain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Performance of the Pro-sp3-TASSER server in CASP8

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Protein structure prediction by pro-Sp3-TASSER.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Protein model refinement using an optimized physics-based all-atom force field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Effects of posttranslational modifications on the structure and dynamics of histone H3 N-terminal Peptide

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Development of a physics-based force field for the scoring and refinement of protein models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

GLYCAM06: a generalizable biomolecular force field. Carbohydrates

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Ab initio protein structure prediction using chunk-TASSER

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Computational methods in protein structure prediction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Development and validation of a modular, extensible docking program: DOCK 5.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Post-translational modifications in the context of therapeutic proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

A new force field (ECEPP-05) for peptides, proteins, and organic molecules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

IPRO: an iterative computational protein library redesign and optimization procedure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

ASTRO-FOLD: A Combinatorial and Global Optimization Framework for Ab Initio Prediction of Three-Dimensional Structures of Proteins from the Amino Acid Sequence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Directed evolution of a genetic circuit

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Automated docking of substrates to proteins by simulated annealing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Isoform-selective inhibition of chrysin towards human cytochrome P450 1A2. Kinetics analysis, molecular docking, and molecular dynamics simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Force field parameters for the simulation of modified histone tails

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Isoform-specific determinants in the HP1 binding to histone 3: insights from molecular simulations.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Force field parameters for S-nitrosocysteine and molecular dynamics simulations of S-nitrosated thioredoxin

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Corynebacterial protein kinase G controls 2-oxoglutarate dehydrogenase activity via the phosphorylation status of the OdhI protein

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3904396

Integrated Computational and Experimental Approach for Lead Optimization and Design of Compstatin Variants with Improved Activity

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24489522

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24489522

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

An all atom force field for simulations of proteins and nucleic acids

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24489522

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT400556V

3 references

25 May 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24489522%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

PubMed publication ID

24489522

2 references