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Periodic rigidity of protein crystal structures
Found in: Computational Advances in Bio and Medical Sciences, IEEE International Conference on
By Pamela Clark,Jessica Grant,Samantha Monastra,Filip Jagodzinski,Ileana Streinu
Issue Date:February 2012
pp. 1-6
We initiate in silico rigidity-theoretical studies of protein crystal structures, with the goal to determine if, and how, the interactions among neighboring crystal cells affect the flexibility of biological unit. We use an efficient graph-based algorithm ...
 
Using rigidity analysis to probe mutation-induced structural changes in proteins
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By Filip Jagodzinski,Jeanne Hardy,Ileana Streinu
Issue Date:November 2011
pp. 432-437
Predicting how a single amino acid substitution affects the stability of a protein structure is a fundamental task in macromolecular modeling. It has relevance to drug design and understanding of disease-causing protein variants. We present KINARI-Mutagen,...
 
Towards a hybrid method for detecting critical protein residues
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Bahar Akbal-Delibas,Filip Jagodzinski,Nurit Haspel
Issue Date:October 2012
pp. 82-85
Some regions in proteins play a critical role in determining their structure and function. Examples include flexible regions such as hinges which allow domain motions, and highly conserved functional interfaces which allow interactions with other proteins....
 
Combining conservation and rigidity methods to detect critical residues in proteins
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Bahar Akbal-Delibas,Filip Jagodzinski,Nurit Haspel
Issue Date:October 2012
pp. 940
The structure and the functionality of proteins are closely related to each other. Therefore, analyzing the structural and dynamical properties of proteins is crucial for understanding their role in the basic biology of organisms. Some specific regions in ...
 
The XML Log Standard for Digital Libraries: Analysis, Evolution, and Deployment
Found in: Digital Libraries, Joint Conference on
By Marcos André Gonçalves, Ganesh Panchanathan, Unnikrishnan Ravindranathan, Aaron Krowne, Edward A. Fox, Filip Jagodzinski, Lillian Cassel
Issue Date:May 2003
pp. 312
We describe current efforts and developments building on our proposal for an XML log standard format for digital library (DL) logging analysis and companion tools. Focus is given to the evolution of formats and tools, based on analysis of deployment in sev...
 
The XML Log Standard for Digital Libraries: Analysis, Evolution, and Deployment
Found in: Digital Libraries, Joint Conference on
By Marcos André Gonçalves, Ganesh Panchanathan, Unnikrishnan Ravindranathan, Aaron Krowne, Edward A. Fox, Filip Jagodzinski, Lillian Cassel
Issue Date:May 2003
pp. 312
We describe current efforts and developments building on our proposal for an XML log standard format for digital library (DL) logging analysis and companion tools. Focus is given to the evolution of formats and tools, based on analysis of deployment in sev...
 
Rigidity and flexibility of protein-nucleic acid complexes
Found in: 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)
By Emily Flynn,Filip Jagodzinski,Sharon Pamela Santana,Ileana Streinu
Issue Date:June 2013
pp. 1-6
The study of protein-nucleic acid complexes is relevant for the understanding of many biological processes, including transcription, translation, replication, and recombination. The individual molecules in such complexes must be rigid enough to allow geome...
   
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