Mu Gao

Research Scientist II

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

Center for the Study of Systems Biology
250 14th Street, NW, Room 145
Atlanta GA, 30318
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


Google Scholar Profile

Publications

Zhou, H, Gao M, Kumar N, Skolnick J.  Submitted.  SUNPRO: Structure and function predictions of proteins from representative organisms. BMC Bioinformatics.
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 Abstract
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 Abstract
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 Abstract
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 Abstract
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 Abstract
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 Abstract
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. Abstract
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. Abstract
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. Abstract
Gao, M, Schulten K.  2006.  Onset of anthrax toxin pore formation.. Biophysical journal. 90(9):3267-79. Abstract
Gao, M, Schulten K.  2004.  Integrin activation in vivo and in silico.. Structure (London, England : 1993). 12(12):2096-8.
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. Abstract
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. Abstract
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. Abstract
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.
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. Abstract
Gao, M, Wilmanns M, Schulten K.  2002.  Steered molecular dynamics studies of titin I1 domain unfolding.. Biophysical journal. 83(6):3435-45. Abstract
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. Abstract
Gao, M, Lu H, Schulten K.  2001.  Simulated refolding of stretched titin immunoglobulin domains.. Biophysical journal. 81(4):2268-77. Abstract
Isralewitz, B, Gao M, Schulten K.  2001.  Steered molecular dynamics and mechanical functions of proteins.. Current opinion in structural biology. 11(2):224-30. Abstract

Skolnick Group

Services
PSIFR
Protein Structure Prediction
chunk-TASSER
MetaTASSER
pro-sp3-TASSER
TASSER
Protein Structure Refinement
BSR
Protein Structure Alignment
Fr-TM-align
iAlign
DNA-binding Prediction
DBD-Threader
DBD-Hunter
DP-dock
Protein Function Prediction
FINDSITE
FINDSITE-metal
EFICAz2.5
Ligand Docking/Screening
FINDSITELHM
Q-DockLHM
Software
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EFICAz2.5
FINDSITE
FINDSITELHM
FINDSITE-metal
Fr-TM-align
iAlign
PULCHRA
TASSER-Lite
Databases
Structure Prediction Libraries
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Human GPCRs
E. coli Proteome
PDB-like Structures
Function Prediction Libraries
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KinomeLHM
X-ReactKIN
Human Proteome
Human DNA Binders
Reference Libraries
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Active Site Templates
Apo/Holo Pairs
Simulations
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E. coli Intracellular Dynamics
PSIFR - a web portal that provides access to TASSER, TASSER-Lite and MetaTASSER and DBD-Hunter, and the enzyme function inference engine EFICaz2.
MetaTASSER - a protein structure prediction server that uses three
state-of-the-art threading methods PROSPECTOR_3, SP3 and SPARKS to identify templates that are selected by 3D-Jury. For targets with no reliable templates, chunk models from chunk-TASSER are also included. SPICKER clustering is used to select the final models from the TASSER trajectory. Detailed atomic models are then built using PULCHRA.
pro-sp3-TASSER - uses a single threading method with multiple scoring to identify templates. Short TASSER runs generate full length models that are selected by TASSER-QA and FTCOM ranking procedures. pro-sp3-TASSER performs better than MetaTASSER for medium/hard targets but is computationally more expensive.
Fr-TM-align - structural alignment program for monomeric proteins that uses the TM-score as the structure comparison metric.
iAlign - structural alignment algorithm for protein-protein interfaces that uses the TM-score as well as a side-chain contact overlap weighted TM-score as the interface comparison metric.
DBD-Threader - a server that predicts DNA-binding protein domains from a protein's sequence.
DBD-Hunter - a server that predicts DNA-binding protein domains given a protein’s structure.
DP-dock - a server that predicts the structure of the DNA/protein complex structure given the tertiary structure of a known DNA-binding protein.
FINDSITE - a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins. Crystal structures as well as protein models can be used as the target structures.
FINDSITE-metal - a simple extension of FINDSITE that predicts metal-binding sites, residues and binding metal preferences from evolutionarily related templates detected by threading. Furthermore, it employs machine learning to significantly improve the prediction accuracy particularly against modeled protein structures.
FINDSITELHM - a homology modeling approach to flexible ligand docking. It uses a collection of common molecule substructures derived from evolutionarily related templates as the reference compounds in similarity-based ligand binding pose prediction.
Q-DockLHM - a low-resolution ligand docking/refinement approach applicable to the modeled structures of target receptors. It uses pocket-specific statistical potentials and harmonic restraints imposed on the binding poses of the common molecule substructures extracted from evolutionarily related proteins.
EFICAz2.5 - an accurate sequence based approach to enzyme function inference.
chunk-TASSER - a protein structure prediction method that combines threading templates from SP3 and ab initio folded chunk structures (three consecutive segments of regular secondary structures).
BSR - Binding Site Refinement employs a new template-based method for the local refinement of ligand-binding regions in protein models using closely as well as distantly related templates identified by threading.
FINDSITE - a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins.
Fr-TM-align - a program for protein structural alignment that uses the TM-score as the structural comparison metric. This is an improved version of Tm-align.
iAlign - a structural alignment algorithm for the protein-protein interface that uses the TM-score as well as a side-chain contact overlap weighted TM-score as the interface comparison metric.
PULCHRA - a program for all-atom reconstruction from the backbone C-alpha atoms.
TASSER-Lite - a comparative protein structure modeling tool.
Human GPCRs - Predicted structures of 907 G protein-coupled receptors in the Human proteome.
Human DNA Binders - DBD-Threader Predictions on the Human proteome. A list of predicted Human DNA-binding proteins their Sequences and predicted 3D models.
E. coli Poteome - Predicted structures of the E. Coli proteome.
PDB-like Structures - A library of 15,000 compact homopolypeptide structures that cover the PDB.
Active Site Templates - Automated Functional Templates (AFT) for Enzyme Active Site Prediction.
Apo/Holo Pairs - Apo/Holo and Holo/Holo protein pairs. The global structures of apo and holo protein.
KinomeLHM - Comprehensive structural and functional characterization of the human kinome by protein structure predication and ligand virtual screening.
Human Proteome - Structure modeling, function annotation and ligand virtual screening of the human proteome.
TASSER - A meta server for protein structure prediction that combines chunk-TASSER, pro-sp3-TASSER and MetaTASSER.
FINDSITELHM - A homology modeling approach to flexible ligand docking. It uses a collection of common molecule substructures derived from evolutionarily related templates as the reference compounds in similarity-based ligand binding pose prediction.
E. coli Intracellular Dynamics - The inside of cells is highly crowded with bio-macromolecules, such as proteins, DNA, RNA. This environment is quite different from the conditions in a test tube that we usually use for analysis of biomolecular functions, where the macromolecular concentration is ~100 times less than inside cells.
X-ReactKIN - Virtual cross-reactivity profiles of the human kinome.