• Publications
  • Influence
KINARI-Web: a server for protein rigidity analysis
TLDR
KINARI-Web is an interactive web server for performing rigidity analysis and visually exploring rigidity properties of proteins. Expand
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The XML log standard for digital libraries: analysis, evolution, and deployment
TLDR
We describe current efforts and developments building on our proposal for an XML log standard for digital library (DL) logging analysis and companion tools, based on analysis of deployment in several DL systems and testbeds. Expand
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Glyceraldehyde-3-phosphate dehydrogenase in neurodegeneration and apoptosis signaling.
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a well-studied glycolytic enzyme that plays a key role in energy metabolism. GAPDH catalyzes the conversion of glyceraldehyde-3-phosphate toExpand
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MotifAnalyzer‐PDZ: A computational program to investigate the evolution of PDZ‐binding target specificity
Recognition of short linear motifs (SLiMs) or peptides by proteins is an important component of many cellular processes. However, due to limited and degenerate binding motifs, prediction of cellularExpand
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Predicting the Effect of Single and Multiple Mutations on Protein Structural Stability
TLDR
We compare and assess the utility of several machine learning methods and their ability to predict the effects of single and double mutations on protein structure and stability. Expand
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Towards a mechanistic view of protein motion
TLDR
We present a method and accompanying simulation results that the large-scale motions of a protein can be simulated based entirely on kinematic considerations. Expand
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Using rigidity analysis to probe mutation-induced structural changes in proteins
TLDR
We present KINARI-Mutagen, a web server for performing in silico mutation experiments on protein structures from the Protein Data Bank. Expand
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Big Holes in Big Data: A Monte Carlo Algorithm for Detecting Large Hyper-Rectangles in High Dimensional Data
TLDR
We present the first algorithm for finding holes in high dimensional data that runs in polynomial time with respect to the number of dimensions. Expand
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Using rigidity analysis to probe mutation-induced structural changes in proteins
TLDR
We present KINARI-Mutagen, a web server for performing in silico mutation experiments on protein structures from the Protein Data Bank. Expand
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An Evolutionary Conservation & Rigidity Analysis Machine Learning Approach for Detecting Critical Protein Residues
TLDR
We present a machine-learning based method for the analysis and prediction of critical residues in proteins. Expand
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