Yi He - Publications

Affiliations: 
2009-2017 Chemistry and Chemical Biology University of New Mexico, Albuquerque, NM, United States 

24 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.546
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  0.56
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  0.425
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  0.517
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  0.582
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  0.523
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  0.527
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  0.471
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  0.346
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  0.427
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  0.559
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  0.496
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  0.49
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  0.523
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  0.526
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  0.552
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  0.465
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  0.503
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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