How DNA is organized in three dimensions inside the cell nucleus and how that affects the ways in which cells access, read and interpret genetic information are among the longest standing questions in cell biology. Using newly developed molecular, genomic, and computational approaches based on the chromosome conformation capture technology (such as 3C, 4C, 5C and Hi-C) the spatial organization of genomes is being explored at unprecedented resolution. Interpreting the increasingly large chromatin interaction datasets is now posing novel challenges. Here we describe several types of statistical and computational approaches that have recently been developed to analyze chromatin interaction data.

/pdf/exploring-the-three-dimensional-organization-of-genomes-36n1pxvxrk.pdf

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

Cellular processes often depend on interactions between proteins and the formation of macromolecular complexes. The impairment of such interactions can lead to deregulation of pathways resulting in disease states, and it is hence crucial to gain insights into the nature of macromolecular assemblies. Detailed structural knowledge about complexes and protein-protein interactions is growing, but experimentally determined three-dimensional multimeric assemblies are outnumbered by complexes supported by non-structural experimental evidence. Here, we aim to fill this gap by modeling multimeric structures by homology, only using amino acid sequences to infer the stoichiometry and the overall structure of the assembly. We ask which properties of proteins within a family can assist in the prediction of correct quaternary structure. Specifically, we introduce a description of protein-protein interface conservation as a function of evolutionary distance to reduce the noise in deep multiple sequence alignments. We also define a distance measure to structurally compare homologous multimeric protein complexes. This allows us to hierarchically cluster protein structures and quantify the diversity of alternative biological assemblies known today. We find that a combination of conservation scores, structural clustering, and classical interface descriptors, can improve the selection of homologous protein templates leading to reliable models of protein complexes.

/pdf/modeling-protein-quaternary-structure-of-homo-and-hetero-2g0611gik0.pdf

Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology

Pore-forming toxins (PFTs) are virulence factors produced by many pathogenic bacteria and have long fascinated structural biologists, microbiologists and immunologists. Interestingly, pore-forming proteins with remarkably similar structures to PFTs are found in vertebrates and constitute part of their immune system. Recently, structural studies of several PFTs have provided important mechanistic insights into the metamorphosis of PFTs from soluble inactive monomers to cytolytic transmembrane assemblies. In this Review, we discuss the diverse pore architectures and membrane insertion mechanisms that have been revealed by these studies, and we consider how these features contribute to binding specificity for different membrane targets. Finally, we explore the potential of these structural insights to enable the development of novel therapeutic strategies that would prevent both the establishment of bacterial resistance and an excessive immune response.

Pore-forming toxins: ancient, but never really out of fashion

UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System

Accurate SAXS profile computation and its assessment by contrast variation experiments.

A set of software tools for building and distributing models of macromolecular assemblies uses an integrative structure modeling approach, which casts the building of models as a computational optimization problem where information is encoded into a scoring function used to evaluate candidate models.

/pdf/putting-the-pieces-together-integrative-modeling-platform-10d7wlnwfc.pdf

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies.

In one aspect, a computer-implemented method for providing individualized portable asset applications may generally include providing access to a master geospatial asset and receiving a user input associated with generating a portable geospatial asset based on the master geospatial asset, wherein the portable geospatial asset corresponds to a data subset of the master geospatial asset. The method may also include generating the portable geospatial asset based on the user input and embedding the portable geospatial asset within an asset application, wherein the asset application includes computer-readable instructions for rendering the portable geospatial asset. In addition, the method may include transmitting the asset application containing the portable geospatial asset to a separate computing device.

System and method for providing individualized portable asset applications

Portable globes may be provided for viewing regions of interest in a Geographical Information System (GIS). A method for providing a portable globe for a GIS may include determining one or more selected regions corresponding to a geographical region of a master globe. The method may further include organizing geospatial data from the master globe based on the selected region and creating the portable globe based on the geospatial data. The portable globe may be smaller in data size than the master globe. The method may include transmitting the portable globe to a local device that may render the selected region at a higher resolution than the remainder of the portable globe in the GIS. A system for providing a portable globe may include a selection module, a fusion module and a transmitter. A system for updating a portable globe may include a packet bundler and a globe cutter.

Portable globe creation for a geographical information system

A computer-implemented method for providing filtered geospatial assets may include providing access to a reference geospatial asset including geospatial data and receiving a filter request to associate a filter with the reference geospatial asset. The filter request may include at least one filter parameter associated with limiting access to a portion of the geospatial data. In addition, the method may include receiving an access request to access a filtered version of the reference geospatial asset using an access point associated with the filter and applying the filter to the reference geospatial asset to generate the filtered version of the reference geospatial asset. The filtered version may provide access to only a portion of the geospatial data contained within the reference geospatial asset.

System and method for providing filtered geospatial assets

A system and method provides recommendations of documents to a user of a document corpus. Document features are extracted and assigned weights, and a profile is likewise created for users. Documents are scored with respect to a given user based at least in part on the document features and the user's profile. The document scores may be adjusted to reflect organizational goals, such as promoting recommendation of newer documents. Based on the scores, recommendations are determined for a given user by identifying the top scores for that user and presented to the user in one of a variety of manners, such as within a web-based user interface, or via email. Interactions of the users with recommendations may be monitored and the recommendations updated accordingly.

Personalized content-based recommendation system with behavior-based learning

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