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Development of Charge-Augmented Three-Point Water Model (CAIPi3P) for Accurate Simulations of Intrinsically Disordered Proteins

https://doi.org/10.3390/ijms21176166
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/chem.201804556openalex-snapshot
Quantitative Binding Behavior of Intrinsically Disordered Proteins to Nanoparticle Surfaces at Individual Residue Level
inferredcites →https://doi.org/10.1002/jcc.20084openalex-snapshot
UCSF Chimera—A visualization system for exploratory research and analysis
inferredcites →https://doi.org/10.1002/pro.2261openalex-snapshot
A decade and a half of protein intrinsic disorder: Biology still waits for physics
inferredcites →https://doi.org/10.1002/prot.10299openalex-snapshot
Refinement of protein structures in explicit solvent
inferredcites →https://doi.org/10.1002/prot.22711openalex-snapshot
Improved side‐chain torsion potentials for the Amber ff99SB protein force field
inferredcites →https://doi.org/10.1002/prot.25025openalex-snapshot
Coarse‐grained modeling of the intrinsically disordered protein Histatin 5 in solution: Monte Carlo simulations in combination with SAXS
inferredcites →https://doi.org/10.1006/jmbi.1997.1044openalex-snapshot
Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin 1 1Edited by P. E. Wright
inferredcites →https://doi.org/10.1007/978-94-015-7658-1_21openalex-snapshot
Interaction Models for Water in Relation to Protein Hydration
inferredcites →https://doi.org/10.1016/j.jmgm.2016.12.014openalex-snapshot
Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method
inferredcites →https://doi.org/10.1016/j.softx.2015.06.001openalex-snapshot
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
inferredcites →https://doi.org/10.1016/j.str.2013.09.014openalex-snapshot
Phosphorylation Drives a Dynamic Switch in Serine/Arginine-Rich Proteins
inferredcites →https://doi.org/10.1021/acs.jcim.5b00043openalex-snapshot
Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins
inferredcites →https://doi.org/10.1021/acs.jcim.5b00308openalex-snapshot
Force-Field Induced Bias in the Structure of Aβ21–30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields
inferredcites →https://doi.org/10.1021/acs.jcim.7b00135openalex-snapshot
The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins
inferredcites →https://doi.org/10.1021/acs.jctc.5b00736openalex-snapshot
Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment
inferredcites →https://doi.org/10.1021/acs.jctc.5b00868openalex-snapshot
Binding of Disordered Peptides to Kelch: Insights from Enhanced Sampling Simulations
inferredcites →https://doi.org/10.1021/acs.jctc.6b00429openalex-snapshot
Molecular Dynamics Simulations of Intrinsically Disordered Proteins: On the Accuracy of the TIP4P-D Water Model and the Representativeness of Protein Disorder Models
inferredcites →https://doi.org/10.1021/acs.jctc.7b00143openalex-snapshot
Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins
inferredcites →https://doi.org/10.1021/acs.jctc.8b00285openalex-snapshot
Universal Implementation of a Residue-Specific Force Field Based on CMAP Potentials and Free Energy Decomposition
inferredcites →https://doi.org/10.1021/acs.jctc.8b01123openalex-snapshot
General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins
inferredcites →https://doi.org/10.1021/acs.jpcb.7b08925openalex-snapshot
Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations
inferredcites →https://doi.org/10.1021/acs.jpcb.8b05797openalex-snapshot
Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain
inferredcites →https://doi.org/10.1021/acs.jpcb.8b09029openalex-snapshot
Computational Studies of Intrinsically Disordered Proteins
inferredcites →https://doi.org/10.1021/acs.jpclett.6b00885openalex-snapshot
Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation
inferredcites →https://doi.org/10.1021/acs.jpclett.9b00850openalex-snapshot
Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties
inferredcites →https://doi.org/10.1021/ct500569bopenalex-snapshot
Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
inferredcites →https://doi.org/10.1021/ct501178zopenalex-snapshot
Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment
inferredcites →https://doi.org/10.1021/ct700200bopenalex-snapshot
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
inferredcites →https://doi.org/10.1021/jp003020wopenalex-snapshot
Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K
inferredcites →https://doi.org/10.1021/jp108618dopenalex-snapshot
Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse
inferredcites →https://doi.org/10.1021/jz501780aopenalex-snapshot
Building Water Models: A Different Approach
inferredcites →https://doi.org/10.1038/srep15449openalex-snapshot
The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments
inferredcites →https://doi.org/10.1063/1.2121687openalex-snapshot
A general purpose model for the condensed phases of water: TIP4P/2005
inferredcites →https://doi.org/10.1063/1.2408420openalex-snapshot
Canonical sampling through velocity rescaling
inferredcites →https://doi.org/10.1063/1.328693openalex-snapshot
Polymorphic transitions in single crystals: A new molecular dynamics method
inferredcites →https://doi.org/10.1063/1.3569563openalex-snapshot
The large quadrupole of water molecules
inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot
Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1063/1.464397openalex-snapshot
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
inferredcites →https://doi.org/10.1073/pnas.1800690115openalex-snapshot
Developing a molecular dynamics force field for both folded and disordered protein states
inferredcites →https://doi.org/10.1093/nar/gku1287openalex-snapshot
Synergic interplay of the La motif, RRM1 and the interdomain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module
inferredcites →https://doi.org/10.1107/s0021889812007662openalex-snapshot
New developments in the ATSAS program package for small-angle scattering data analysis
inferredcites →https://doi.org/10.1107/s0021889895007047openalex-snapshot
CRYSOL– a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates
inferredcites →https://doi.org/10.1111/cbdd.13342openalex-snapshot
Intrinsically disordered protein‐specific force field CHARMM 36 IDPSFF
inferredcites →https://doi.org/10.1146/annurev.biochem.71.090501.150003openalex-snapshot
The La Protein
inferredcites →https://doi.org/10.1158/0008-5472.can-15-2308openalex-snapshot
Identification of RNA-Binding Protein LARP4B as a Tumor Suppressor in Glioma
inferredcites →https://doi.org/10.1261/rna.051441.115openalex-snapshot
LARP4B is an AU-rich sequence associated factor that promotes mRNA accumulation and translation
inferredcites →https://doi.org/10.3390/biom9040146openalex-snapshot
Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins
inferredcites →https://doi.org/10.7717/peerj.5125openalex-snapshot
Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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