Center for the Study of Systems Biology

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Mu Gao

Senior Research Scientist

mugao

Ph.D., University of Illinois at Urbana-Champaign, 2003

Center for the Study of Systems Biology
950 Atlantic Drive, Room 2147
Atlanta GA, 30332, Mail Code: 2000
Tel: (404) 407-8988
Fax: (404) 385-7478
mu.gao@gatech.edu

Research Interests

  • Protein-DNA, Protein-RNA, protein-protein interactions
  • Protein structure/function prediction and design
  • Macromolecular assembly
  • Molecular dynamics simulations
  • Mechanobiology
  • Drug discovery

My Google Scholar Profile

Publications

von Beck, T, Navarrete K, Arce N A, Gao, M, Dale G A, Davis-Gardner M E, Floyd K, Hernandez L M, Mullick N, Vanderheiden A, Skountzou I, Kuchipudi S V, Saravanan R, Li R, Skolnick J, Suthar M S, Jacob J. A wild boar cathelicidin peptide derivative inhibits severe acute respiratory syndrome coronavirus-2 and its drifted variants. Scientific Reports 2023: 13: 14650. https://doi.org/10.1038/s41598-023-41850-7. PDF

Davidson, R, Coletti M, Gao, M, Piatkowski B, Sreedasyam A, Quadir F, Weston D J, Schmutz, J, Cheng J, Skolnick J, Parks J, Sedova A. 2023. Predicted structural proteome of Sphagnum divinum and annotation with proteome-scale structural alignment. Bioinformatics 39(8): btad511. https://doi.org/10.1093/bioinformatics/btad511. PDF

Gao, M, Nakajima An D, Skolnick J. 2022. Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria. eLife 11:e82885. https://doi.org/10.7554/eLife.82885. PDF

Gao, M, Nakajima An D, Skolnick J. 2022. Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria. bioRxiv 2022.08.25.505253; doi: https://doi.org/10.1101/2022.08.25.505253. PDF
*This article is a preprint and has not been certified by peer review.

Gao, M, Nakajima An D, Parks J M, Skolnick J. 2022. AF2Compex Predicts direct physical interactions in multimeric proteins with deep learning. Nat Commun. 13, 1774. doi.org/10.1038/s41467-022-29394-2. PDF

Gao, M, Nakajima An D, Parks J M, Skolnick J. 2021. Predicting direct physical interactions in multimeric proteins with deep learning. bioRxiv 2021.11.09.467949; doi: https://doi.org/10.1101/2021.11.09.467949. PDF
*This article is a preprint and has not been certified by peer review.

Skolnick, J, Gao M, Zhou H, Singh S. 2021. AlphaFold 2: Why it works and its implications for understanding the relationships of protein sequence, structure and function. J. Chem. Inf. Model. 61: 10: 4827-4831. doi: 10.1021/acs.jcim.1c01114 PDF

Gao, M, Lund-Andersen P, Morehead A, Mahmud S, Chen C, Chen X, Giri N, Roy R S, Quadir F, Effler T C, Prout R, Abraham S, Skolnick J, Cheng J, Sedova A. 2021. High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function. 2021 IEEE/ACM Workshop on Machine Learning in High Performance Computing Environments (MLHPC), 2021, pp. 46-57, doi: 10.1109/MLHPC54614.2021.00010. PDF

Gao, M, Skolnick, J. 2021. A general framework to learn tertiary structure for protein sequence annotation. Front. Bioinform. 1: 689960. doi: 10.3389/fbinf.2021.689960. PDF

Gao, M, Skolnick, J. 2021. A general framework to learn tertiary structure for protein sequence annotation. bioRxiv 2021.04.01.438098; doi: https://doi.org/10.1101/2021.04.01.438098. PDF
*This article is a preprint and has not been certified by peer review.

Skolnick, J, Gao, M. 2021. On the emergence of homochirality and life itself. The Biochemist. 43(1): 4-12. doi:10.1042/BIO20210002 PDF

Skolnick, J, Gao, M. 2021. The role of local versus nonlocal physicochemical restraints in determining protein native structure. Curr Opin Struct Bio. 68:1–8.  doi: 10.1016/j.sbi.2020.10.008. PDF

Gao, M, Skolnick, J. 2021. A novel sequence alignment algorithm based on deep learning of the protein folding code. Bioinformatics. 37(4): 490-496. doi: 10.1093/bioinformatics/btaa810. PDF

Cao, H, Jin M, Gao M, Zhou H, Tao YJ, Skolnick J. 2020. Differential kinase activity of ACVR1 G328V and R206H mutations with implications to possible TβRI pathway cross-talk in diffuse intrinsic pontine glioma. Scientific Reports. 10: 6140. doi: 10.1038/s41598-020-63061-0. PDF

Skolnick, J, Zhou H, Gao M. 2019. On the possible origin of protein homochirality, structure and biochemical function. PNAS. 116(52): 26571–26579. https://doi.org/10.1073/pnas.1908241116. PDF

Gao, M, Zhou H, Skolnick J. 2019. DESTINI: A deep-learning approach to contact-driven protein structure prediction. Scientific Reports. 9: 3514. https://doi.org/10.1038/s41598-019-40314-1. PDF

Cao, H, Gao M, Zhou H, Skolnick J. 2018. The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release. Communications Biology. 1:226: https://doi.org/10.1038/s42003-018-0236-y. PDF

Zhou, H, Gao M, Skolnick J. 2018. ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations. PlosOne. 13(5):e0196849. PDF

Eimon, PM, Ghannad-Rezaie M, De Rienzo G, Allalou A, Wu Y, Gao M, Roy A, Skolnick J, Yanik M F. 2018. Brain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects. Nature Communications. 9:219 PDF

Snell, T, Johnson R, Matthews AB, Zhou H, Gao M, Skolnick J. 2018. Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers. Biogerontology. PDF

Zhou, H, Gao M, Skolnick J. 2016. ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures. PLOS ONE. 11(3):e0150965. PDF

Skolnick, J, Gao M, Zhou H. 2016. How special is the biochemical function of native proteins? F1000Research. 5:207. PDF

Snell, TW, Johnston RK, Srinivasan B, Zhou H, Gao M, Skolnick J. 2016. Repurposing FDA-approved drugs for anti-aging therapies. Biogerontology. 17(5-6):907-920. PDF

Zhou, H, Gao M, Skolnick J. 2015. Comprehensive prediction of drug-protein interactions and side effects for the human proteome. Scientific Reports. 5:11090. PDF

Boles, RG, Hornung HA, Moody AE, Ortiz TB, Wong SA, Eggington JM, Stanley CM, Gao M, Zhou H, McLaughlin S et al. 2015. Hurt, tired and queasy: Specific variants in the ATPase domain of the TRAP1 mitochondrial chaperone are associated with common, chronic “functional” symptomatology including pain, fatigue and gastrointestinal dysmotility. Mitochondrion. 23:64-70. PDF

Gao M, Zhou H, Skolnick J. 2015. Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis. Structure. 23(7):1362-1369.  PDF

Skolnick, J, Gao M, Roy A, Srinivasan B, Zhou H. 2015. Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function.Bioorganic & Medicinal Chemistry Letters. 25:1163-1170. PDF

Skolnick, J, Gao M, Zhou H. 2014. On the Role of Physics and Evolution in Dictating Protein Structure and Function. Israel Journal of Chemistry. 54(8-9):1176-1188. PDF

Skolnick, J, Gao M. 2013. Interplay of physics and evolution in the likely origin of protein biochemical function. Proceedings of the National Academy of Sciences. 110(23):9344-9349.  PDF

Gao M, Skolnick J. 2013. APoc: large-scale identification of similar protein pockets. Bioinformatics. 29(5):597-604.  PDF

Skolnick, J, Zhou H, Gao M. 2013. Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Current opinion in structural biology. 23(2):191-7.  PDF

Gao M, Skolnick J. 2013. A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins. PLoS Computational Biology. 9(10):e1003302.  PDF

Gao M, Skolnick J. 2012. The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation. Proceedings of the National Academy of Sciences. 109(10):3784-3789. PDF

Gao M, Skolnick J. 2011. New benchmark metrics for protein-protein docking methods. Proteins: Structure, Function, and Bioinformatics. 79(5):1623-1634. PDF

Brylinski, M, Gao M, Skolnick J. 2011. Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function Physical Chemistry Chemical Physics. 13 (38):17044-17055.  PDF

Pandit, S B, Brylinski M, Zhou H, Gao M, Arakaki AK, Skolnick J. 2010. PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (Oxford, England). 26(5):687-8. PDF

Gao M, Skolnick J. 2010. iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics (Oxford, England). 26(18):2259-65.  PDF Supplementary Data

Gao M, Skolnick J. 2010. 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(52):22517-22. PDF Supplementary Data

Gao M, Skolnick J. 2009. A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PLoS computational biology. 5(11):e1000567. PDF Supplementary Data

Gao M, Skolnick J. 2009. From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. PLoS computational biology. 5(3):e1000341.  PDF

Gao M, Skolnick J. 2008. DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic acids research. 36(12):3978-92. PDF Supplementary Data

Puklin-Faucher, E, Gao M, Schulten K, Vogel V. 2006. How the headpiece hinge angle is opened: New insights into the dynamics of integrin activation. The Journal of cell biology. 175(2):349-60. PDF

Gao, M, Sotomayor M, Villa E, Lee EH, Schulten K. 2006. Molecular mechanisms of cellular mechanics. Physical chemistry chemical physics: PCCP. 8(32):3692-706. PDF

Lee, EH, Gao M, Pinotsis N, Wilmanns M, Schulten K. 2006. Mechanical strength of the titin Z1Z2-telethonin complex. Structure (London, England: 1993). 14(3):497-509. PDF

Gao, M, Schulten K. 2006. Onset of anthrax toxin pore formation. Biophysical journal. 90(9):3267-79. PDF

Gao, M, Schulten K. 2004. Integrin activation in vivo and in silico. Structure (London, England: 1993). 12(12):2096-8. PDF

Craig, D, Gao M, Schulten K, Vogel V. 2004. Structural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force. Structure (London, England: 1993). 12(11):2049-58. PDF

Craig, D, Gao M, Schulten K, Vogel V. 2004. Tuning the mechanical stability of fibronectin type III modules through sequence variations. Structure (London, England : 1993). 12(1):21-30. PDF

Gao, M, Craig D, Lequin O, Campbell ID, Vogel V, Schulten K. 2003. 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(25):14784-9. PDF

Tajkhorshid, E, Aksimentiev A, Balabin I, Gao M, Isralewitz B, Phillips JC, Zhu F, Schulten K. 2003. Large scale simulation of protein mechanics and function. Advances in protein chemistry. 66:195-247. PDF

Gao, M, Lu H, Schulten K. 2002. Unfolding of titin domains studied by molecular dynamics simulations. Journal of muscle research and cell motility. 23(5-6):513-21. PDF

Gao, M, Wilmanns M, Schulten K. 2002. Steered molecular dynamics studies of titin I1 domain unfolding. Biophysical journal. 83(6):3435-45. PDF

Gao, M, Craig D, Vogel V, Schulten K. 2002. Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics. Journal of molecular biology. 323(5):939-50. PDF

Gao, M, Lu H, Schulten K. 2001. Simulated refolding of stretched titin immunoglobulin domains. Biophysical journal. 81(4):2268-77. PDF

Isralewitz, B, Gao M, Schulten K. 2001. Steered molecular dynamics and mechanical functions of proteins. Current opinion in structural biology. 11(2):224-30. PDF

  • Skolnick Research Group
    • Jeffrey Skolnick
    • Hiteshri Chudasama
    • Mu Gao
    • Jessica Gilmore Forness
    • Bartosz Ilkowski
    • Lilya Matyunina
    • Yusaku “Nick” Nitta
    • Nandita Puri
    • Nilavrah Sensarma
    • Hongyi Zhou
    • Former Group Members
  • Software and Services
    • Services
      • DESTINI
      • DR. PRODIS
      • ENTPRISE
      • ENTPRISE-X
      • FINDSITEcomb
      • FINDSITEcomb2.0
      • FRAGSITE
      • FRAGSITE2
      • Know-GENE
      • LeMeDISCO
      • MEDICASCY
      • MOATAI-VIR
      • PHEVIR
    • Downloads
      • AF2Complex
      • APoc
      • Cavitator
      • DBD-Hunter
      • DBD-Threader
      • EFICAz2.5
      • Fr-TM-align
      • GOAP
      • iAlign
      • IS-score
      • LIGSIFT
      • PULCHRA
      • SAdLSA
    • Databases
      • Apo and Holo Pairs
      • New Human GPCR Modeling and Virtual Screening
      • PDB-like Structures
    • Simulations
      • E. coli Intracellular Dynamics

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