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DALIX: Optimal DALI Protein Structure Alignment
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Inken Wohlers,Rumen Andonov,Gunnar W. Klau
Issue Date:January 2013
pp. 26-36
We present a mathematical model and exact algorithm for optimally aligning protein structures using the DALI scoring model. This scoring model is based on comparing the interresidue distance matrices of proteins and is used in the popular DALI software too...
 
Antilope—A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Gunnar W. Klau, Knut Reinert, Knut Reinert, Gunnar W. Klau, Knut Reinert, Sandro Andreotti, Sandro Andreotti, Sandro Andreotti
Issue Date:March 2012
pp. 385-394
Peptide sequencing from mass spectrometry data is a key step in proteome research. Especially de novo sequencing, the identification of a peptide from its spectrum alone, is still a challenge even for state-of-the-art algorithmic approaches. In this paper,...
     
DALIX: Optimal DALI Protein Structure Alignment
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Gunnar W. Klau, Inken Wohlers, Rumen Andonov
Issue Date:January 2013
pp. 26-36
We present a mathematical model and exact algorithm for optimally aligning protein structures using the dali scoring model. This scoring model is based on comparing the interresidue distance matrices of proteins and is used in the popular dali software too...
     
The HuGS platform: a toolkit for interactive optimization
Found in: Proceedings of the Working Conference on Advanced Visual Interfaces (AVI '02)
By Gunnar W. Klau, Guy T. Schafer, Joe Marks, Michael Mitzenmacher, Neal Lesh
Issue Date:May 2002
pp. 19-24
In this paper we develop a generalized approach to visualizing and controlling an optimization process. Our framework, called Human-Guided Search, actively involves people in the process of optimization. We provide simple and general visual metaphors that ...
     
Investigating human-computer optimization
Found in: Proceedings of the SIGCHI conference on Human factors in computing systems: Changing our world, changing ourselves (CHI '02)
By Gunnar W. Klau, Neal Lesh, Stacey D. Scott
Issue Date:April 2002
pp. 155-162
Scheduling, routing, and layout tasks are examples of hard optimization problems with broad application in industry. Past research in this area has focused on algorithmic issues. However, this approach neglects many important human-computer interaction iss...
     
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