| 1. |
- Keasar, Chen, et al.
(författare)
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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
- 2018
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research.
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| 3. |
- Ghosh, Soma, et al.
(författare)
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Rule Based Modeling of Iron Homeostasis in Tuberculosis
- 2010
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Ingår i: The Eighth Asia Pacific Bioinformatics Conference, Bangalore, India (APBC2010).
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Mycobacterium tuberculosis (Mtb), which causes Tuberculosis (TB), has evolved into manydrug resistant forms, and in symbiosis with AIDS and other diseases, has become a dreadedpathogen world-wide. In an attempt to find new drugs, researchers have turned to the study ofiron homeostasis in TB: iron is an important resource that Mtb steals from its host, and isinvolved in the manifestation of virulence. We have formally encoded the relevant molecularinteractions described in the literature, yielding a program to simulate these aspects of ironmetabolism in Mtb, in the host, and in the interaction between the two. Iron acquisition viasiderophores is featured in detail.The Kappa modeling language we use represents molecular interactions compactly by rules,these being generalisations of chemical equations. The Kappa tool tells us syntactically howthe reactions are related, so we can see which play a central role, and which are comparativelyisolated. Our simulation results, both pathways and concentrations of species, match thosedescribed in the literature. Our program can therefore be used as an unambiguousrepresentation to anchor discussions about iron and TB, and to predict the results ofhypothetical perturbations that might be of use in the search for new drugs. For example, theresults of changing the infection level are as expected.A future possibility would be to combine our model with a genetic algorithm to suggest waysin which Mtb might evolve resistance to planned interventions.
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