3260299
The Protein Non-Folding Problem: Amino Acid Determinants of Intrinsic Order and Disorder
To investigate the determinants of protein order and disorder, three primary and one derivative database of intrinsically disordered proteins were compiled. The segments in each primary database were characterized by one of the following: X-ray crystallography, nuclear magnetic resonance (NMR), or circular dichroism (CD). The derivative database was based on homology. The three primary disordered databases have a combined total of 157 proteins or segments of length.30 with 18,010 residues, while the derivative database contains 572 proteins from 32 families with 52,688 putatively disordered residues. For the four disordered databases, the amino acid compositions were compared with those from a database of ordered structure. Relative to the ordered protein, the intrinsically disordered segments in all four databases were significantly depleted in W, C, F, I, Y, V, L and N, significantly enriched in A, R, G, Q, S, P, E and K, and inconsistently different in H, M, T, and D, suggesting that the first set be called order-promoting and the second set disorder-promoting. Also, 265 amino acid properties were ranked by their ability to discriminate order and disorder and then pruned to remove the most highly correlated pairs. The 10 highest-ranking properties after pruning consisted of 2 residue contact scales, 4 hydrophobicity scales, 3 scales associated with.-sheets and one polarity scale. Using these 10 properties for comparisons of the 3 primary databases suggests that disorder in all 3 databases is very similar, but with those characterized by NMR and CD being the most similar, those by CD and X-ray being next, and those by NMR and X-ray being the least similar.
12227821
DisProt: a database of protein disorder
UNLABELLED
The Database of Protein Disorder (DisProt) is a curated database that provides structure and function information about proteins that lack a fixed three-dimensional (3D) structure under putatively native conditions, either in their entirety or in part. Starting from the central premise that intrinsic disorder is an important structural class of protein and in order to meet the increasing interest thereof, DisProt is aimed at becoming a central repository of disorder-related information. For each disordered protein, the database includes the name of the protein, various aliases, accession codes, amino acid sequence, location of the disordered region(s), and methods used for structural (disorder) characterization. If applicable, most entries also list the biological function(s) of each disordered region, how each region of disorder is used for function, as well as provide links to PubMed abstracts and major protein databases.


AVAILABILITY
www.disprot.org
8482892
Improving Sequence Alignments For Intrinsically Disordered Proteins
Here we analyze sequence alignments for intrinsically disordered proteins. For 55 disordered protein families we measure the performance of different scoring matrices and propose one adjusted to disordered regions. An iterative algorithm of realigning sequences and recalculating matrices is designed and tested. For each matrix we also test a wide range of gap penalties. Results show an improvement in the ability to detect and discriminate related disordered proteins whose average sequence identity with the other family members is below 50%.
829668
Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regions
Using proteins with both disordered and ordered regions collected through literature searches and database scanning, we assembled a set of 24-residue long segments centered on their order/disorder boundaries as well as a larger set of non-boundary segments consisting of either order or disorder. We analyzed position-specific amino acid compositions around the order/disorder boundaries and found more than thirty significant (p < 0.05) compositional differences between boundary and non-boundary data. From this analysis, we constructed several logistic regression predictors of order/disorder boundaries using slightly different data modeling approaches. Exact boundary prediction accuracies were estimated to be in the range from 74% to 80% for the different predictors.
31238264
The populated web: Browsing, searching and inhabiting the WWW using collaborative virtual environments
This paper presents new approaches for accessing the World Wide Web using multi-user three dimensional spaces, or collaborative virtual environments (CVEs.) The major sections of the paper deal with the aspects of browsing and navigating, searching, populating and displaying information within, and about the WWW. The methods described are illustrated with examples of working applications developed by the authors which together present an image of a possible future for Web access and collaboration based around the Web and its contents.
13531439
Combining Type Theory and Untyped Set Theory
We describe a dependent type theory with proof irrelevance. Within this framework, we give a representation of a form of Mac Lane set theory and discuss automated support for constructing proofs within this set theory. One of the novel aspects of the representation is that one is allowed to use any class (in the set theory) as a type (in the type theory). Such class types allow a natural way of representing partial functions (e.g., the first and second operators on the class of Kuratowski ordered pairs). We also discuss how automated search can be used to construct proofs. In particular, the first-order prover Vampire can be called to solve a challenge problem (the injective Cantor Theorem) which is notoriously difficult for higher-order automated provers.
529377
Encoding Functional Relations in Scunak
We describe how a set-theoretic foundation for mathematics can be encoded in the new system Scunak. We then discuss an encoding of the construction of functions as functional relations in untyped set theory. Using the dependent type theory of Scunak, we can define object level application and lambda abstraction operators (in the spirit of higher-order abstract syntax) mediating between functions in the (meta-level) type theory and (object-level) functional relations. The encoding has also been exported to Automath and Twelf.
16390848
A Fully Projective Formulation to Improve the Accuracy of Lowe's Pose-Estimation Algorithm
Both the original version of David Lowe's influential and classic algorithm for tracking known objects and a reformulation of it implemented by Ishiiet al. rely on (different) approximated imaging models. Removing their simplifying assumptions yields a fully projective solution with significantly improved accuracy and convergence, and arguably better computation-time properties.
12173886
VR-VIBE: A Virtual Environment for Co-operative Information Retrieval
We present a virtual reality application called VR-VIBE which is intended to support the co-operative browsing and filtering of large document stores. VR-VIBE extends a visualisation approach proposed in a previous two dimensional system called VIBE into three dimensions, allowing more information to be visualised at one time and supporting more powerful styles of interaction, The essence of VR-VIBE is that multiple users can explore the results of applying several simultaneous queries to a corpus of documents. By arranging the queries into a spatial framework, the system shows the relative attraction of each document to each query by its spatial position and also shows the absolute relevance of each document to all of the queries. Users may then navigate the space, select individual documents, control the display according to a dynamic relevance threshold and dynamically drag the queries to new positions to see the effect on the document space. Co-operative browsing is supported by directly embodying users and providing them with the ability to interact over live audio connections and to attach brief textual annotations to individual documents. Finally, we conclude with some initial observations gleaned from our experience of constructing VR-VIBE and using it in the laboratory setting.