31663632
MACiE: a database of enzyme reaction mechanisms
SUMMARY
MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction.


AVAILABILITY
http://www-mitchell.ch.cam.ac.uk/macie/.
1936302
Communication and re-use of chemical information in bioscience
The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.
6478208
Chemistry in Bioinformatics
AbstractChemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols.
18575731
Classifying the World Anti-Doping Agency's 2005 Prohibited List Using the Chemistry Development Kit Fingerprint
We used the freely available Chemistry Development Kit (CDK) fingerprint to classify 5235 representative molecules taken from ten banned classes in the 2005 World Anti-Doping Agency’s (WADA) prohibited list, including molecules taken from the corresponding activity classes in the MDL Drug Data Report (MDDR). We used both Random Forest and k-Nearest Neighbours (kNN) algorithms to generate classifiers. The kNN classifiers withk = 1 gave a very slightly better Matthews Correlation Coefficient than the Random Forest classifiers; the latter, however, predicted fewer false positives. The performance of kNN classifiers tended to decline with increasing k. The performance of the CDK fingerprint is essentially equivalent to that of Unity 2D. Our results suggest that it will be possible to use freely available chemoinformatics tools to aid the fight against drugs in sport, while minimising the risk of wrongfully penalising innocent athletes.
14904191
Games and the Impossibility of Realizable Ideal Functionality
A cryptographic primitive or a security mechanism can be specified in a variety of ways, such as a condition involving a game against an attacker, construction of an ideal functionality, or a list of properties that must hold in the face of attack. While game conditions are widely used, an ideal functionality is appealing because a mechanism that is indistinguishable from an ideal functionality is therefore guaranteed secure in any larger system that uses it. We relate ideal functionalities to games by defining the set of ideal functionalities associated with a game condition and show that under this definition, which reflects accepted use and known examples, bit commitment, a form of group signatures, and some other cryptographic concepts do not have any realizable ideal functionality.
1569108
Distributed Credential Chain Discovery in Trust Management
We introduce a simple Role-based Trust-management language RT0 and a set-theoretic semantics for it. We also introduce credential graphs as a searchable representation of credentials in RT0 and prove that reachability in credential graphs is sound and complete with respect to the semantics of RT0. Based on credential graphs, we give goal-directed algorithms to do credential chain discovery in RT0, both when credential storage is centralized and when credential storage is distributed. A goal-directed algorithm begins with an access-control query and searches for credentials relevant to the query, while avoiding considering the potentially very large number of credentials that are unrelated to the access-control decision at hand. This approach provides better expected-case performance than bottom-up algorithms. We show how our algorithms can be applied to SDSI 2.0 (the 'SDSI' part of SPKI/SDSI 2.0).Our goal-directed, distributed chain discovery algorithm finds and retrieves credentials as needed. We prove that the algorithm is correct by proving that the algorithm is sound and complete with respect to the credential graph composed of the credentials it retrieves, and that the algorithm retrieves all credentials that constitute a traversable chain. We further introduce a storage type system for RT0, which guarantees traversability of chains when credentials are well typed. This type system can also help improve search efficiency by guiding search in the right direction, making distributed chain discovery with large number of credentials feasible.
28274388
Query-Sensitive Ray Shooting
Ray (segment) shooting is the problem of determining the first intersection between a ray (directed line segment) and a collection of polygonal or polyhedral obstacles. In order to process queries efficiently, the set of obstacle polyhedra is usually preprocessed into a data structure. In this paper we propose a query-sensitive data structure for ray shooting, which means that the performance of our data structure depends on the local geometry of obstacles near the query segment. We measure the complexity of the local geometry near the segment by a parameter called the simple cover complexity, denoted by scc(s) for a segment s. Our data structure consists of a subdivision that partitions the space into a collection of polyhedral cells, each of O(1) complexity. We answer a segment shooting query by wallking along the segment through the subdivision. Our first result is that, for any fixed dimension d, there exists a simple hierarchical subdivision in which no query segment s intersects more than O(scc(s)) cells. Our second result shows that in two dimensions such a subdivision of size O(n) can be constructed in time O(nlogn), where n is the total number of vertices in all the obstacles.
7795941
Specifying and verifying hardware for tamper-resistant software
We specify a hardware architecture that supports tamper-resistant software by identifying an "idealized" model, which gives the abstracted actions available to a single user program. This idealized model is compared to a concrete "actual" model that includes actions of an adversarial operating system. The architecture is verified by using a finite-state enumeration tool (a model checker) to compare executions of the idealized and actual models. In this approach, software tampering occurs if the system can enter a state where one model is inconsistent with the other in performing the verification, we detected a replay attack scenario and were able to verify the security of our solution to the problem. Our methods were also able to verify that all actions in the architecture are required, as well as come up with a set of constraints on the operating system to guarantee liveness for users.
2518390
A Compositional Logic for Proving Security Properties of Protocols
We present a logic for proving security properties of protocols that use nonces (randomly generated numbers that uniquely identify a protocol session) and public-key cryptography. The logic, designed around a process calculus with actions for each possible protocol step, consists of axioms about protocol actions and inference rules that yield assertions about protocols composed of multiple steps. Although assertions are written using only steps of the protocol, the logic is sound in a stronger sense: each provable assertion about an action or sequence of actions holds in any run of the protocol that contains the given actions and arbitrary additional actions by a malicious attacker. This approach lets us prove security properties of protocols under attack while reasoning only about the sequence of actions taken by honest parties to the protocol. The main security-specific parts of the proof system are rules for reasoning about the set of messages that could reveal secret data and an invariant ride called the "honesty rule".