scholarly article | Q13442814 |
P8978 | DBLP publication ID | journals/jcisd/SongLC17 |
P356 | DOI | 10.1021/ACS.JCIM.7B00135 |
P932 | PMC publication ID | 5731455 |
P698 | PubMed publication ID | 28448138 |
P50 | author | Haifeng Chen | Q75721314 |
Ray Luo | Q47098696 | ||
Dong Song | Q58808132 | ||
P2093 | author name string | Dong Song | |
Hai-Feng Chen | |||
P2860 | cites work | Intrinsically unstructured proteins and their functions | Q22061731 |
A series of PDB related databases for everyday needs | Q24613221 | ||
Comparison of simple potential functions for simulating liquid water | Q26778447 | ||
The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix | Q27621171 | ||
A Combinatorial NMR and EPR Approach for Evaluating the Structural Ensemble of Partially Folded Proteins | Q27662113 | ||
Folding of the Tau Protein on Microtubules | Q27701048 | ||
Structure of ubiquitin refined at 1.8 A resolution | Q27728512 | ||
Solution Structure of the KIX Domain of CBP Bound to the Transactivation Domain of CREB: A Model for Activator:Coactivator Interactions | Q27748755 | ||
All-atom empirical potential for molecular modeling and dynamics studies of proteins | Q27860468 | ||
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features | Q27860675 | ||
The Amber biomolecular simulation programs | Q27860745 | ||
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation | Q27860944 | ||
Comparison of multiple Amber force fields and development of improved protein backbone parameters | Q27861040 | ||
Intrinsically disordered protein | Q28191444 | ||
Intrinsic disorder in cell-signaling and cancer-associated proteins | Q28207698 | ||
Roles of phosphorylation and helix propensity in the binding of the KIX domain of CREB-binding protein by constitutive (c-Myb) and inducible (CREB) activators | Q28219104 | ||
Conformational preferences in the Ser133-phosphorylated and non-phosphorylated forms of the kinase inducible transactivation domain of CREB | Q28910220 | ||
The protein non-folding problem: amino acid determinants of intrinsic order and disorder | Q73658941 | ||
Alzheimer's-disease-associated conformation of intrinsically disordered tau protein studied by intrinsically disordered protein liquid-phase competitive enzyme-linked immunosorbent assay | Q79325388 | ||
Observation of beta-sheet aggregation in a gas-phase tau-peptide dimer | Q83261087 | ||
A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions | Q29031294 | ||
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew | Q29396077 | ||
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes | Q29397708 | ||
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations | Q29547631 | ||
BioMagResBank | Q29614807 | ||
Sequence complexity of disordered protein | Q29616420 | ||
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. | Q30341299 | ||
Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L. | Q30362385 | ||
Protein structural and surface water rearrangement constitute major events in the earliest aggregation stages of tau. | Q31034284 | ||
Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins | Q31155071 | ||
ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins | Q33824917 | ||
Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins | Q33851634 | ||
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association | Q34503099 | ||
The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development | Q34577841 | ||
Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology | Q34645831 | ||
Intrinsically disordered proteins in cellular signalling and regulation. | Q35510300 | ||
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born | Q35948015 | ||
Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. | Q36558058 | ||
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. | Q36766916 | ||
Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein. | Q37218609 | ||
Intrinsically disordered proteins and intrinsically disordered protein regions | Q38194194 | ||
Small-angle scattering studies of intrinsically disordered proteins and their complexes. | Q38994238 | ||
Calibration of the angular dependence of the amide proton-C alpha proton coupling constants, 3JHN alpha, in a globular protein. Use of 3JHN alpha for identification of helical secondary structure | Q39339655 | ||
CHARMM36m: an improved force field for folded and intrinsically disordered proteins | Q40299880 | ||
Binding induced folding in p53-MDM2 complex | Q41816238 | ||
Intrinsic disorder in putative protein sequences | Q42210557 | ||
Correction to Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association | Q42545304 | ||
New force field on modeling intrinsically disordered proteins. | Q44063793 | ||
Improved treatment of the protein backbone in empirical force fields. | Q44735024 | ||
Solution structure of the KIX domain of CBP bound to the transactivation domain of c-Myb | Q44799099 | ||
A folding-after-binding mechanism describes the recognition between the transactivation domain of c-Myb and the KIX domain of the CREB-binding protein | Q46062204 | ||
RNA recognition by an isolated α helix | Q46325121 | ||
Automatic assignment of the intrinsically disordered protein Tau with 441-residues | Q53311821 | ||
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules | Q55918670 | ||
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems | Q56750591 | ||
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States | Q56873339 | ||
Structural biology: Breaking the protein rules | Q57071963 | ||
Residual Dipolar Couplings in Short Peptides Reveal Systematic Conformational Preferences of Individual Amino Acids | Q57080210 | ||
P433 | issue | 5 | |
P921 | main subject | force field | Q1341441 |
P304 | page(s) | 1166-1178 | |
P577 | publication date | 2017-04-27 | |
P1433 | published in | Journal of Chemical Information and Modeling | Q3007982 |
P1476 | title | The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins | |
P478 | volume | 57 |
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