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Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab Initio Protein Structure Prediction
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Kevin Molloy,Sameh Saleh,Amarda Shehu
Issue Date:September 2013
pp. 1162-1175
Adequate sampling of the conformational space is a central challenge in ab initio protein structure prediction. In the absence of a template structure, a conformational search procedure guided by an energy function explores the conformational space, gather...
 
A robotics-inspired method to sample conformational paths connecting known functionally-relevant structures in protein systems
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Kevin Molloy,Amarda Shehu
Issue Date:October 2012
pp. 56-63
Characterization of transition trajectories that take a protein between different functional states is an important yet challenging problem in computational biology. Approaches based on Molecular Dynamics can obtain the most detailed and accurate informati...
 
A tree-based search to bias sampling of protein decoy conformations
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Kevin Molloy,Amarda Shehu
Issue Date:October 2012
pp. 978
A central challenge in ab-initio structure prediction is the attainment of a large diverse ensemble of decoy conformations at low resolution so that subsequent refinement of selected decoys at higher resolution can identify the native structure among them ...
 
Mapping conformational pathways between known functional protein states
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Kevin Molloy,Amarda Shehu
Issue Date:October 2012
pp. 971
Understanding and elucidating the conformational rearrangements that protein systems undergo to transition between different functional states is an important but challenging problem in computational biology [1]. Wet-lab techniques allow resolving represen...
 
Assembly of low-energy protein conformations with heterogeneous fragments
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By Kevin Molloy,Amarda Shehu
Issue Date:November 2011
pp. 991-993
The most successful ab-initio protein structure prediction methods employ fragment-based assembly. This technique is usually implemented in the context of a Metropolis Monte Carlo template. Fragment length is an important consideration, as it controls the ...
 
Higher-order representations of protein structure space
Found in: 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)
By Kevin Molloy,M. Jennifer Van,Daniel Barbara,Amarda Shehu
Issue Date:June 2013
pp. 1-2
Fragment-based representations of protein structure have recently been proposed to identify remote homologs with reasonable accuracy. The representations have also been shown through PCA to elucidate low-dimensional maps of protein structure space. In this...
   
Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab Initio Protein Structure Prediction
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Amarda Shehu, Kevin Molloy, Sameh Saleh
Issue Date:September 2013
pp. 1162-1175
Adequate sampling of the conformational space is a central challenge in ab initio protein structure prediction. In the absence of a template structure, a conformational search procedure guided by an energy function explores the conformational space, gather...
     
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