| Year |
Citation |
Score |
| 2023 |
Li T, Hendrix E, He Y. Simple and Effective Conformational Sampling Strategy for Intrinsically Disordered Proteins Using the UNRES Web Server. The Journal of Physical Chemistry. B. 127: 2177-2186. PMID 36827446 DOI: 10.1021/acs.jpcb.2c08945 |
0.308 |
|
| 2020 |
Pineda LIG, Milko LN, He Y. Performance of CHARMM36m with modified water model in simulating intrinsically disordered proteins: a case study Biophysics Reports. 6: 80-87. DOI: 10.1007/S41048-020-00107-W |
0.353 |
|
| 2018 |
Sieradzan AK, Giełdoń A, Yin Y, He Y, Scheraga HA, Liwo A. A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. Journal of Computational Chemistry. PMID 30306573 DOI: 10.1002/Jcc.25571 |
0.501 |
|
| 2018 |
He Y, Nagpal S, Sadqi M, de Alba E, Muñoz V. Glutton: A tool for generating structural ensembles of partly disordered proteins from chemical shifts. Bioinformatics (Oxford, England). PMID 30184055 DOI: 10.1093/Bioinformatics/Bty755 |
0.552 |
|
| 2018 |
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, ... ... He Y, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports. 8: 9939. PMID 29967418 DOI: 10.1038/s41598-018-26812-8 |
0.39 |
|
| 2017 |
He Y, Maisuradze GG, Yin Y, Kachlishvili K, Rackovsky S, Scheraga HA. Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 28143938 DOI: 10.1073/Pnas.1621344114 |
0.482 |
|
| 2016 |
Krupa P, Mozolewska MA, Wiśniewska M, Yin Y, He Y, Sieradzan AK, Ganzynkowicz R, Lipska AG, Karczyńska A, Ślusarz M, Ślusarz R, Giełdoń A, Czaplewski C, Jagieła D, Zaborowski B, et al. Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinformatics (Oxford, England). PMID 27378298 DOI: 10.1093/Bioinformatics/Btw404 |
0.528 |
|
| 2015 |
He Y, Liwo A, Scheraga HA. Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach. The Journal of Chemical Physics. 143: 243111. PMID 26723596 DOI: 10.1063/1.4932082 |
0.481 |
|
| 2015 |
Yin Y, Sieradzan AK, Liwo A, He Y, Scheraga HA. Physics-based potentials for coarse-grained modeling of protein-DNA interactions. Journal of Chemical Theory and Computation. 11: 1792-1808. PMID 26052263 DOI: 10.1021/Ct5009558 |
0.486 |
|
| 2015 |
He Y, Rackovsky S, Yin Y, Scheraga HA. Alternative approach to protein structure prediction based on sequential similarity of physical properties. Proceedings of the National Academy of Sciences of the United States of America. 112: 5029-32. PMID 25848034 DOI: 10.1073/Pnas.1504806112 |
0.446 |
|
| 2015 |
He Y, Liwo A, Scheraga HA. Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach Journal of Chemical Physics. 143. DOI: 10.1063/1.4932082 |
0.322 |
|
| 2015 |
Yin Y, Sieradzan AK, Liwo A, He Y, Scheraga HA. Physics-based potentials for coarse-grained modeling of protein-DNA interactions Journal of Chemical Theory and Computation. 11: 1792-1808. DOI: 10.1021/ct5009558 |
0.381 |
|
| 2014 |
Liwo A, Baranowski M, Czaplewski C, Go?a? E, He Y, Jagie?a D, Krupa P, Maciejczyk M, Makowski M, Mozolewska MA, Niadzvedtski A, O?dziej S, Scheraga HA, Sieradzan AK, Slusarz R, et al. A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions. Journal of Molecular Modeling. 20: 2306. PMID 25024008 DOI: 10.1007/S00894-014-2306-5 |
0.511 |
|
| 2014 |
Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, et al. WeFold: a coopetition for protein structure prediction. Proteins. 82: 1850-68. PMID 24677212 DOI: 10.1002/Prot.24538 |
0.464 |
|
| 2014 |
Liwo JA, Sieradzan AK, He Y, Krupa P, Czaplewski CR, Krokhotin A, Niemi AJ, Scheraga HA. Origin of the Architecture of Biological Macromolecules - A Mean-Field Perspective Biophysical Journal. 106: 256a. DOI: 10.1016/J.Bpj.2013.11.1506 |
0.457 |
|
| 2013 |
He Y, Mozolewska MA, Krupa P, Sieradzan AK, Wirecki TK, Liwo A, Kachlishvili K, Rackovsky S, Jagiela D, Åšlusarz R, Czaplewski CR, OÅ‚dziej S, Scheraga HA. Lessons from application of the UNRES force field to predictions of structures of CASP10 targets. Proceedings of the National Academy of Sciences of the United States of America. 110: 14936-41. PMID 23980156 DOI: 10.1073/Pnas.1313316110 |
0.485 |
|
| 2013 |
He Y, Maciejczyk M, OÅ‚dziej S, Scheraga HA, Liwo A. Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix. Physical Review Letters. 110: 098101. PMID 23496746 DOI: 10.1103/Physrevlett.110.098101 |
0.486 |
|
| 2011 |
Zhou R, He Y, Xiao Y. Multi-nucleation and vectorial folding pathways of large helix protein Computational Biology and Chemistry. 35: 169-173. PMID 21704263 DOI: 10.1016/J.Compbiolchem.2011.04.004 |
0.358 |
|
| 2011 |
Liwo A, He Y, Scheraga HA. Coarse-grained force field: general folding theory. Physical Chemistry Chemical Physics : Pccp. 13: 16890-901. PMID 21643583 DOI: 10.1039/C1Cp20752K |
0.505 |
|
| 2011 |
He Y, Liwo A, Weinstein H, Scheraga HA. PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics. Journal of Molecular Biology. 405: 298-314. PMID 21050858 DOI: 10.1016/J.Jmb.2010.10.051 |
0.439 |
|
| 2009 |
He Y, Chen C, Xiao Y. United-Residue (UNRES) Langevin Dynamics Simulations of trpzip2 Folding Journal of Computational Biology. 16: 1719-1730. PMID 20047493 DOI: 10.1089/Cmb.2008.0070 |
0.317 |
|
| 2009 |
He Y, Zhou R, Huang Y, Xiao Y. Brief Communication: Foldable subunits of helix protein Computational Biology and Chemistry. 33: 325-328. PMID 19616477 DOI: 10.1016/J.Compbiolchem.2009.06.001 |
0.357 |
|
| 2009 |
He Y, Xiao Y, Liwo A, Scheraga HA. Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. Journal of Computational Chemistry. 30: 2127-35. PMID 19242966 DOI: 10.1002/Jcc.21215 |
0.467 |
|
| 2009 |
HE Y, ZHOU R, XIAO Y. STUDY OF FOLDING BEHAVIORS OF A SIX-HELIX PROTEIN BY ab initio MOLECULAR DYNAMICS FOLDING SIMULATIONS OF UNRES International Journal of Modern Physics C. 20: 373-382. DOI: 10.1142/S0129183109013686 |
0.356 |
|
| 2005 |
Zhang M, Chen C, He Y, Xiao Y. Improvement on a simplified model for protein folding simulation. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 051919. PMID 16383657 DOI: 10.1103/Physreve.72.051919 |
0.344 |
|
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