Area of Research

Dr. Daisuke Kihara
Principal Investigator

Our research interests lie in the area of bioinformatics. We employ computational methods to elucidate intertwined relationships between protein/gene sequences, structure, function, interactions, genome, and pathways. The ultimate goal of our research projects is to obtain new, comprehensive understanding of how structures and functions are coded in molecular sequences and how functions of molecules are orchestrated in a cell.

Specifically, we develop and apply novel computational methods for...

  • Predicting protein structure from sequence
  • Predicting protein function from sequence and structure
  • Predicting protein-protein and protein-ligand interactions
  • Predicting functional sites in sequences
  • Genome-scale function and structure annotation
  • Analyzing functional units in networks

More information can be found on our research projects page here.

Research Highlights

3D-SURFER 2.0 is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. It can compare the protein surface of a single chain, domain, or complex against databases of protein chains, domains, complexes, or a combination of all three, in the latest PDB. Two types of protein structures can now be compared: all-atom-surface and backbone-atom-surface. The server can also accepts a batch job for a large number of database searches. The databases are weekly updated in an automatic way. Visit the server or read the paper on Proteins.
The protein docking suite developed by our group includes programs to perform protein-protein docking prediction, multiple protein docking, as well as protein docking prediction using predicted protein-protein interfaces. The Linux binaries can be downloaded here
ESG is our new sequence similarity-based protein function prediction server. In essence, it further applies PFP iteratively and obtains superior performance in terms of prediction accuracy. Visit the server to submit a sequence or read the paper in Bioinformatics. ESG annotates query sequences with Gene Ontology terms by assigning probability to each annotation. Statistical framework of ESG improves the prediction accuracy by iteratively taking into account the neighborhood of query protein in the similarity based sequence space.
PFP is our sequence similarity-based protein function prediction server designed to predict GO annotations for a query protein sequence beyond what can be found by searching conventional databases. Visit the server to submit a sequence or read the paper on Protein Science. PFP has achieved the highest total score among participating servers in a function prediciton contest held at AFP-SIG'05, ISMB 2005, and also was the best method in the head-to-head perfomance comparison in the function prediciton category at CASP7.

Recent News

Follow us on Twitter!Follow kiharalab on Twitter News Archives are available here.

  • 1 postdoc position is available. Please see here
  • Xuejiao Kang (CS) joined our lab. Welcome, Xuejiao!
  • Lillian Liu got Best Abstract Award at Undergrad Research Poster Symposium, Purdue University! Congratulations, Lillian!
  • Chao Yuan defended his MS thesis. Congratulations, Chao!
  • Dr. Choi Youn Im, postdoc researcher, joined our lab. Welcome Choi!
  • "Multi-LZerD: Multiple protein docking for asymmetric complexes" by Juan Esquivel-Rodriguez & D. Kihara accepted on Proteins.
  • "Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors" by Juan Esquivel-Rodriguez & D. Kihara accepted on J. Phys. Chemistry.
  • Ross VerHeul (the PULSe program)started rotation. Welcome!
  • "Formyl-coenzyme A (CoA):oxalate CoA-transferase from the acidophile Acetobacter aceti has a distinctive electrostatic surface and inherent acid stability" by Mullins,Starks, Francois, Sael, Kihara, & Kappock accepted on Protein Science.
  • Juan Esquivel-Rodriguez got the 1st Place Award at the Sigma Xi grad poster competition at Purdue! Congratulations! His poster was on "Macromolecular structure modeling and electron microscopy fitting using 3D Zernike descriptors".


Kihara Bioinformatics Laboratory is always looking for new people to join the lab. Our current list of openings is available here.