Min-yi Shen, Ph.D. - Publications

Affiliations: 
2002 University of Chicago, Chicago, IL 
Area:
statistical mechanics of polymers in the liquid phase, protein dynamics aggregation, and folding, equilibrium aggregation phenomena, and molecular electronic structure

18 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
2008 Eramian D, Eswar N, Shen MY, Sali A. How well can the accuracy of comparative protein structure models be predicted? Protein Science : a Publication of the Protein Society. 17: 1881-93. PMID 18832340 DOI: 10.1110/ps.036061.108  0.48
2008 Eswar N, Eramian D, Webb B, Shen MY, Sali A. Protein structure modeling with MODELLER. Methods in Molecular Biology (Clifton, N.J.). 426: 145-59. PMID 18542861 DOI: 10.1007/978-1-60327-058-8_8  0.48
2007 Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using MODELLER. Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. Unit 2.9. PMID 18429317 DOI: 10.1002/0471140864.ps0209s50  0.48
2006 Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using Modeller. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 5.6. PMID 18428767 DOI: 10.1002/0471250953.bi0506s15  0.48
2006 Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A. Structural modeling of protein interactions by analogy: application to PSD-95. Plos Computational Biology. 2: e153. PMID 17096593 DOI: 10.1371/journal.pcbi.0020153  1
2006 Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Science : a Publication of the Protein Society. 15: 2507-24. PMID 17075131 DOI: 10.1110/ps.062416606  0.48
2006 Colubri A, Jha AK, Shen MY, Sali A, Berry RS, Sosnick TR, Freed KF. Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. Journal of Molecular Biology. 363: 835-57. PMID 16982067 DOI: 10.1016/j.jmb.2006.08.035  1
2006 Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA. A composite score for predicting errors in protein structure models. Protein Science : a Publication of the Protein Society. 15: 1653-66. PMID 16751606 DOI: 10.1110/ps.062095806  1
2006 Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS. Protein complex compositions predicted by structural similarity. Nucleic Acids Research. 34: 2943-52. PMID 16738133 DOI: 10.1093/nar/gkl353  1
2006 Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research. 34: D291-5. PMID 16381869 DOI: 10.1093/nar/gkj059  1
2005 Shen MY, Freed KF. A simple method for faster nonbonded force evaluations. Journal of Computational Chemistry. 26: 691-8. PMID 15754302 DOI: 10.1002/jcc.20211  1
2003 Zaman MH, Shen MY, Berry RS, Freed KF, Sosnick TR. Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides. Journal of Molecular Biology. 331: 693-711. PMID 12899838 DOI: 10.1016/S0022-2836(03)00765-4  1
2003 Cui B, Shen MY, Freed KF. Folding and misfolding of the papillomavirus E6 interacting peptide E6ap. Proceedings of the National Academy of Sciences of the United States of America. 100: 7087-92. PMID 12771374 DOI: 10.1073/pnas.0431214100  1
2003 Fernández A, Shen MY, Colubri A, Sosnick TR, Berry RS, Freed KF. Large-scale context in protein folding: villin headpiece. Biochemistry. 42: 664-71. PMID 12534278 DOI: 10.1021/bi026510i  1
2003 Shen MY, Freed KF. Long time dynamics of Met-enkephalin: Tests of mode-coupling theory and implicit solvent models Journal of Chemical Physics. 118: 5143-5156. DOI: 10.1063/1.1544554  1
2003 Dudowicz J, Freed KF, Shen MY. Hydration structure of met-enkephalin: A molecular dynamics study Journal of Chemical Physics. 118: 1989-1995. DOI: 10.1063/1.1531612  1
2003 Zaman MH, Shen MY, Berry RS, Freed KF. Computer simulation of Met-enkephalin using explicit atom and united atom potentials: Similarities, differences, and suggestions for improvement Journal of Physical Chemistry B. 107: 1685-1691. DOI: 10.1021/jp026994s  1
2002 Shen MY, Freed KF. All-atom fast protein folding simulations: the villin headpiece. Proteins. 49: 439-45. PMID 12402354 DOI: 10.1002/prot.10230  1
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