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- 2Proteins
- 13D structure
- 1Associative classification
- 1Crystallization
- 1DNA-binding prediction
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Associative classification, linguistic entity relationship extraction, and description-logic representation of biomedical knowledge applied to MEDLINE
DownloadFall 2009
MEDLINE, a large and constantly increasing collection of biomedical article references, has been the source of numerous investigations related to textual information retrieval and knowledge capture, including article categorization, bibliometric analysis, semantic query answering, and biological...
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Computational support systems for prediction and characterization of protein crystallization outcomes
DownloadFall 2013
Analysis of protein structures may reveal their function, regulation and interactions. Almost 90% of the known protein structures were solved using X-ray crystallography; however, many more structures remain unsolved. Protein Structure Initiative (PSI) project was created to speed up structure...
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Spring 2018
Intrinsically disordered regions (IDRs) in proteins lack stable three dimensional structure under physiological conditions. IDRs are prevalent in nature, functionally important, and difficult to characterize experimentally due to their unstructuredness. As a result, many computational methods...
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Spring 2016
MicroRNAs (miRNAs) are short (~21 nucleotides) endogenous noncoding RNAs. They are widespread post-transcriptional regulators in eukaryotes that bind target messenger RNAs (mRNAs) and regulate the protein expression levels. MiRNAs have attracted substantial amount of research attention and...
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Large-scale Characterization Of Intrinsic Disorder And High-throughput Prediction Of RNA, DNA and Protein Binding Mediated By Intrinsic Disorder
DownloadFall 2014
Intrinsically disordered proteins lack stable 3D structures in vivo, are functionally important, and are very common in nature. In the past three decades, many studies focused on prediction of intrinsic disorder from protein sequence, estimation of its abundance, and analyses of its functional...
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Fall 2010
Fuzzy Cognitive Maps (FCMs) are a widely used, neuro-fuzzy based qualitative approach for the modeling of dynamic systems, which allow for both static and dynamic analyses. They are capable of modeling complex systems with nonlinearities and unknown physical behaviour. FCMs describe a given...
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Prediction and Characterization of DNA and RNA Binding Residues from Protein Sequence: state-of-the-art, novel predictors and proteome-scale analysis
DownloadFall 2016
Interactions between proteins and DNA/RNA play vital roles in many cellular processes and yet many of them remain to be found and characterized. Many computational methods have been developed to predict from protein sequences which parts of the proteins (so called interacting residues) are...
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Sequence-based prediction and characterization of disorder-to-order transitioning binding sites in proteins
DownloadSpring 2012
Molecular Recognition Feature (MoRF) regions are disordered binding sites that become structured upon binding. MoRFs are implicated in important biological processes, including signaling and regulation. However, only a limited number of experimentally validated MoRFs is known, which motivates...