Research Topic

Towards Integrating Protein Sequence, Structure, Function & Therapeutics Discovery for Collaborative Research

About this Research Topic

The advent of web-based software enables open source tools to interoperate as well as converge, and, in doing so, accelerate interdisciplinary collaborative research. We can then begin to seamlessly bridge the fields of genetics, bioinformatics, biochemistry, biophysics and physiology. However, to realize the full potential of integrative biology, collaborative research tools and platforms are needed to facilitate open sharing of both data and analyses. This also requires a self-sustainable community of developers and researchers working in computational biology from diverse disciplines.

Collaborative research is increasingly inter-disciplinary but its full potential has to be unlocked. A large fraction of the domain knowledge and data still exists in silos. Projects that try to span different domains run into many practical challenges of data integration and analysis. In life sciences, collaborative platforms have the potential to connect those silos and cross-fertilize knowledge to enable solutions of pressing scientific questions spanning disparate domains between the clinic (physiology, genetics, therapeutics) and the bench (molecular biology) with an increasing presence of data and computers (computational biology, data science) that now span multiple fields (biochemistry, biophysics, genomics) and diverse cellular as well as molecular data, from sequence to structure. A pertinent example being the identification of a highly infectious virus strain during the pandemic: the identification in quasi-real time of the viral genomic sequence, the determination of its structure and the accelerated design of new vaccines and anti-virals through structure-based design, with a 10-fold reduction in development time.

Many patients and therapeutic areas await such progress in the discovery of drugs, vaccines, and cell therapies. The need to bridge the gap between genetics and structure-based (or at a minimum structure-informed) therapeutic design, requires the development of collaborative platforms and tools that bridge data - and scientists - across many disciplines, streamline data analyses, and enable interactive collaboration over the web. A major goal in developing collaboration tools is the seamless sharing of both data and analyses. Data is either a starting point or an endpoint of any elementary analysis, the analysis being the collaborative and discursive element, and now it can be offered over the web as simple as exchanging hyperlinks. For example, a scientific discussion can be enriched and sustained through the seamless exchange of both data and analyses through hyperlinks. Beyond research, the web-based integration of data and analysis also enables multi-disciplinary education and training of the next generation of scientists. This helps establish the sustainability of multidisciplinary research in the future.

One of the many ways to build bridges across different research domains - and foster collaborative research between scientists - is through regular community-based events, such as hackathons that cross-pollinate data, ideas, and knowledge in developing methods, tools, and shared analysis platforms. This maintains continuity in project themes as well as helps build the next generation of tools from the ground up to catalyze interdisciplinary research. Hackathons are also an efficient way to prototype and test new ideas and software.

We are soliciting manuscripts on open source methods, algorithms and software tools being developed as part of existing collaborations and/or community events such as hackathons, focused on the analysis and integration of molecular data, with data spanning multiple scales of biology covering genomics (biological sequences), bioinformatics, biochemistry, biophysics (biomolecular structure and interactions), and therapeutics.
We welcome manuscripts addressing unmet needs for analysis and collaboration tools that:
- Bridge sequence-structure-function analysis;
- Analyze molecular properties and interactions;
- Analyze large datasets of sequences and structures;
- Visualize 3D molecular structures and interactions in new ways, especially in 2D for uncovering nature’s design principles
- Annotate sequence-topology-structure patterns and properties;
- Extend collaborative research and data sharing mechanisms;
- We also solicit manuscripts exploring direct applications of these and existing tools in the innovative analyses of biomolecules.


Keywords: integrative biology, collaborative research tools, data visualization, sequence analysis, data sharing


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

The advent of web-based software enables open source tools to interoperate as well as converge, and, in doing so, accelerate interdisciplinary collaborative research. We can then begin to seamlessly bridge the fields of genetics, bioinformatics, biochemistry, biophysics and physiology. However, to realize the full potential of integrative biology, collaborative research tools and platforms are needed to facilitate open sharing of both data and analyses. This also requires a self-sustainable community of developers and researchers working in computational biology from diverse disciplines.

Collaborative research is increasingly inter-disciplinary but its full potential has to be unlocked. A large fraction of the domain knowledge and data still exists in silos. Projects that try to span different domains run into many practical challenges of data integration and analysis. In life sciences, collaborative platforms have the potential to connect those silos and cross-fertilize knowledge to enable solutions of pressing scientific questions spanning disparate domains between the clinic (physiology, genetics, therapeutics) and the bench (molecular biology) with an increasing presence of data and computers (computational biology, data science) that now span multiple fields (biochemistry, biophysics, genomics) and diverse cellular as well as molecular data, from sequence to structure. A pertinent example being the identification of a highly infectious virus strain during the pandemic: the identification in quasi-real time of the viral genomic sequence, the determination of its structure and the accelerated design of new vaccines and anti-virals through structure-based design, with a 10-fold reduction in development time.

Many patients and therapeutic areas await such progress in the discovery of drugs, vaccines, and cell therapies. The need to bridge the gap between genetics and structure-based (or at a minimum structure-informed) therapeutic design, requires the development of collaborative platforms and tools that bridge data - and scientists - across many disciplines, streamline data analyses, and enable interactive collaboration over the web. A major goal in developing collaboration tools is the seamless sharing of both data and analyses. Data is either a starting point or an endpoint of any elementary analysis, the analysis being the collaborative and discursive element, and now it can be offered over the web as simple as exchanging hyperlinks. For example, a scientific discussion can be enriched and sustained through the seamless exchange of both data and analyses through hyperlinks. Beyond research, the web-based integration of data and analysis also enables multi-disciplinary education and training of the next generation of scientists. This helps establish the sustainability of multidisciplinary research in the future.

One of the many ways to build bridges across different research domains - and foster collaborative research between scientists - is through regular community-based events, such as hackathons that cross-pollinate data, ideas, and knowledge in developing methods, tools, and shared analysis platforms. This maintains continuity in project themes as well as helps build the next generation of tools from the ground up to catalyze interdisciplinary research. Hackathons are also an efficient way to prototype and test new ideas and software.

We are soliciting manuscripts on open source methods, algorithms and software tools being developed as part of existing collaborations and/or community events such as hackathons, focused on the analysis and integration of molecular data, with data spanning multiple scales of biology covering genomics (biological sequences), bioinformatics, biochemistry, biophysics (biomolecular structure and interactions), and therapeutics.
We welcome manuscripts addressing unmet needs for analysis and collaboration tools that:
- Bridge sequence-structure-function analysis;
- Analyze molecular properties and interactions;
- Analyze large datasets of sequences and structures;
- Visualize 3D molecular structures and interactions in new ways, especially in 2D for uncovering nature’s design principles
- Annotate sequence-topology-structure patterns and properties;
- Extend collaborative research and data sharing mechanisms;
- We also solicit manuscripts exploring direct applications of these and existing tools in the innovative analyses of biomolecules.


Keywords: integrative biology, collaborative research tools, data visualization, sequence analysis, data sharing


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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Submission Deadlines

12 October 2021 Abstract
15 December 2021 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

12 October 2021 Abstract
15 December 2021 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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