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Mu Gao, Ph.D. - Publications

Affiliations: 
2003 University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
Area:
theoretical biophysics
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39 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
2022 Gao M, Nakajima An D, Skolnick J. Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria. Elife. 11. PMID 36576775 DOI: 10.7554/eLife.82885  0.306
2022 Gao M, Nakajima An D, Parks JM, Skolnick J. AF2Complex predicts direct physical interactions in multimeric proteins with deep learning. Nature Communications. 13: 1744. PMID 35365655 DOI: 10.1038/s41467-022-29394-2  0.314
2019 Skolnick J, Zhou H, Gao M. On the possible origin of protein homochirality, structure, and biochemical function. Proceedings of the National Academy of Sciences of the United States of America. PMID 31822617 DOI: 10.1073/Pnas.1908241116  0.374
2019 Gao M, Zhou H, Skolnick J. DESTINI: A deep-learning approach to contact-driven protein structure prediction. Scientific Reports. 9: 3514. PMID 30837676 DOI: 10.1038/S41598-019-40314-1  0.357
2016 Zhou H, Gao M, Skolnick J. ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures. Plos One. 11: e0150965. PMID 26982818 DOI: 10.1371/Journal.Pone.0150965  0.33
2016 Skolnick J, Gao M, Zhou H. How special is the biochemical function of native proteins? F1000research. 5. PMID 26962440 DOI: 10.12688/F1000Research.7374.1  0.445
2015 Liu Y, Yang Y, Gao M, Pan H. Tailoring Thermodynamics and Kinetics for Hydrogen Storage in Complex Hydrides towards Applications. Chemical Record (New York, N.Y.). PMID 26638824 DOI: 10.1002/tcr.201500224  0.313
2015 Gao M, Zhou H, Skolnick J. Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis. Structure (London, England : 1993). PMID 26027735 DOI: 10.1016/J.Str.2015.03.028  0.32
2015 Skolnick J, Gao M, Roy A, Srinivasan B, Zhou H. Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function. Bioorganic & Medicinal Chemistry Letters. 25: 1163-70. PMID 25690787 DOI: 10.1016/J.Bmcl.2015.01.059  0.404
2014 Skolnick J, Gao M, Zhou H. On the role of physics and evolution in dictating protein structure and function. Israel Journal of Chemistry. 54: 1176-1188. PMID 25484448 DOI: 10.1002/Ijch.201400013  0.448
2013 Gao M, Skolnick J. A comprehensive survey of small-molecule binding pockets in proteins. Plos Computational Biology. 9: e1003302. PMID 24204237 DOI: 10.1371/Journal.Pcbi.1003302  0.423
2013 Skolnick J, Gao M. Interplay of physics and evolution in the likely origin of protein biochemical function. Proceedings of the National Academy of Sciences of the United States of America. 110: 9344-9. PMID 23690621 DOI: 10.1073/Pnas.1300011110  0.438
2013 Skolnick J, Zhou H, Gao M. Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Current Opinion in Structural Biology. 23: 191-7. PMID 23415854 DOI: 10.1016/J.Sbi.2013.01.009  0.328
2013 Gao M, Skolnick J. APoc: large-scale identification of similar protein pockets. Bioinformatics (Oxford, England). 29: 597-604. PMID 23335017 DOI: 10.1093/Bioinformatics/Btt024  0.403
2012 Gao M, Skolnick J. The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation. Proceedings of the National Academy of Sciences of the United States of America. 109: 3784-9. PMID 22355140 DOI: 10.1073/Pnas.1117768109  0.433
2012 Gao M, Skolnick J. On the Structural Space of Protein-Protein Interfaces Biophysical Journal. 102: 608a. DOI: 10.1016/J.Bpj.2011.11.3315  0.417
2011 Brylinski M, Gao M, Skolnick J. Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function. Physical Chemistry Chemical Physics : Pccp. 13: 17044-55. PMID 21655593 DOI: 10.1039/C1Cp21140D  0.434
2011 Gao M, Skolnick J. New benchmark metrics for protein-protein docking methods. Proteins. 79: 1623-34. PMID 21365685 DOI: 10.1002/Prot.22987  0.332
2010 Gao M, Skolnick J. Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. Proceedings of the National Academy of Sciences of the United States of America. 107: 22517-22. PMID 21149688 DOI: 10.1073/Pnas.1012820107  0.391
2010 Gao M, Skolnick J. iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics (Oxford, England). 26: 2259-65. PMID 20624782 DOI: 10.1093/Bioinformatics/Btq404  0.426
2010 Pandit SB, Brylinski M, Zhou H, Gao M, Arakaki AK, Skolnick J. PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (Oxford, England). 26: 687-8. PMID 20080513 DOI: 10.1093/Bioinformatics/Btq006  0.395
2009 Gao M, Skolnick J. A threading-based method for the prediction of DNA-binding proteins with application to the human genome. Plos Computational Biology. 5: e1000567. PMID 19911048 DOI: 10.1371/Journal.Pcbi.1000567  0.383
2009 Gao M, Skolnick J. From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. Plos Computational Biology. 5: e1000341. PMID 19343221 DOI: 10.1371/Journal.Pcbi.1000341  0.352
2009 Gao M, Skolnick J. In Silico Study Of Nonspecific DNA-protein Encounter Complexes Biophysical Journal. 96: 64a. DOI: 10.1016/J.Bpj.2008.12.230  0.339
2008 Gao M, Skolnick J. DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Research. 36: 3978-92. PMID 18515839 DOI: 10.1093/Nar/Gkn332  0.374
2006 Puklin-Faucher E, Gao M, Schulten K, Vogel V. How the headpiece hinge angle is opened: New insights into the dynamics of integrin activation. The Journal of Cell Biology. 175: 349-60. PMID 17060501 DOI: 10.1083/Jcb.200602071  0.501
2006 Gao M, Sotomayor M, Villa E, Lee EH, Schulten K. Molecular mechanisms of cellular mechanics. Physical Chemistry Chemical Physics : Pccp. 8: 3692-706. PMID 16896432 DOI: 10.1039/B606019F  0.727
2006 Lee EH, Gao M, Pinotsis N, Wilmanns M, Schulten K. Mechanical strength of the titin Z1Z2-telethonin complex. Structure (London, England : 1993). 14: 497-509. PMID 16531234 DOI: 10.1016/J.Str.2005.12.005  0.544
2006 Gao M, Schulten K. Onset of anthrax toxin pore formation. Biophysical Journal. 90: 3267-79. PMID 16473908 DOI: 10.1529/Biophysj.105.079376  0.487
2004 Gao M, Schulten K. Integrin activation in vivo and in silico. Structure (London, England : 1993). 12: 2096-8. PMID 15576022 DOI: 10.1016/J.Str.2004.11.005  0.458
2004 Craig D, Gao M, Schulten K, Vogel V. Structural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force. Structure (London, England : 1993). 12: 2049-58. PMID 15530369 DOI: 10.1016/J.Str.2004.09.009  0.536
2004 Craig D, Gao M, Schulten K, Vogel V. Tuning the mechanical stability of fibronectin type III modules through sequence variations. Structure (London, England : 1993). 12: 21-30. PMID 14725762 DOI: 10.1016/J.Str.2003.11.024  0.524
2003 Gao M, Craig D, Lequin O, Campbell ID, Vogel V, Schulten K. Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates. Proceedings of the National Academy of Sciences of the United States of America. 100: 14784-9. PMID 14657397 DOI: 10.1073/Pnas.2334390100  0.513
2003 Tajkhorshid E, Aksimentiev A, Balabin I, Gao M, Isralewitz B, Phillips JC, Zhu F, Schulten K. Large scale simulation of protein mechanics and function. Advances in Protein Chemistry. 66: 195-247. PMID 14631820 DOI: 10.1016/S0065-3233(03)66006-7  0.705
2002 Gao M, Lu H, Schulten K. Unfolding of titin domains studied by molecular dynamics simulations. Journal of Muscle Research and Cell Motility. 23: 513-21. PMID 12785101 DOI: 10.1023/A:1023466608163  0.55
2002 Gao M, Wilmanns M, Schulten K. Steered molecular dynamics studies of titin I1 domain unfolding. Biophysical Journal. 83: 3435-45. PMID 12496110 DOI: 10.1016/S0006-3495(02)75343-5  0.523
2002 Gao M, Craig D, Vogel V, Schulten K. Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics. Journal of Molecular Biology. 323: 939-50. PMID 12417205 DOI: 10.1016/S0022-2836(02)01001-X  0.514
2001 Gao M, Lu H, Schulten K. Simulated refolding of stretched titin immunoglobulin domains. Biophysical Journal. 81: 2268-77. PMID 11566797 DOI: 10.1016/S0006-3495(01)75874-2  0.484
2001 Isralewitz B, Gao M, Schulten K. Steered molecular dynamics and mechanical functions of proteins. Current Opinion in Structural Biology. 11: 224-30. PMID 11297932 DOI: 10.1016/S0959-440X(00)00194-9  0.736
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