Ron Poet

One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins.

Gamma-turns may be defined by a hydrogen bond between the carbonyl group of one amino acid residue and the amino group of the acid two residues ahead in the sequence. They occur as two types, inverse gamma-turns and classic gamma-turns (classic gamma-turns are usually called just gamma-turns but we prefer to add the adjective classic to distinguish them from the word gamma-turn, referring collectively to both). Of the two, classic gamma-turns are less common and are considered by all authors to be extreme rarities in proteins. However, we find that a number do occur in a sample of proteins of known three-dimensional structure. One occurs at the edge of the second hypervariable region of the light chain in some immunoglobulins. All classic gamma-turns except one are associated with a reversal in the main chain direction. In most cases, the turn lies at the loop end of a beta-hairpin. By contrast, inverse gamma-turns, although giving rise to a kink in the chain, rarely occur within beta-hairpins and are seldom situated at a position of reversal, by 180 degrees, in chain direction.

Coulombic attractions between partially chargedmain-chain atoms stabilise the right-handed twist found in most β-strands

The use of Lennard-Jones potentials gives rise to an expected energy distribution for main-chain polypeptide conformations in the Ramachandran plot that matches well the observed distribution of phi, psi values in high-resolution proteins. The position of the energy minimum in the beta-strand conformation region is situated where there is a substantial contribution from the electrostatic attraction between the partial charge of the carbonyl carbon atom of one amino acid residue and that of the carbonyl oxygen atom of an adjacent residue. This attraction gives rise to a preference for the right-twisted beta-strand conformation compared with the left-twisted conformation. The majority of beta-sheets are twisted, almost always in one direction. Looking along a single strand, the twist is to the right. This twist also helps provide a rationale for the characteristic topology of the strand-helix-strand unit often observed in alpha/beta proteins. The electrostatic explanation for the twist we propose has not, to our knowledge, been explicitly suggested previously. The factor that has been most widely proposed to explain the twist is steric hindrance involving side-chain atoms. We provide evidence that the electrostatic effect is of comparable significance. Right-twisted beta-strands are geometrically closely related to polyproline II helices and to collagen helices, both of which are left-handed. Short regions of polyproline II type helices, which are sometimes, but not always, rich in proline residues, are common at protein surfaces. We point out that these helices are stabilised by the same carbonyl-carbonyl interactions as in right-twisted beta-strands.

Loops, bulges, turns and hairpins in proteins

Abstract The structures of commonly occurring loop motifs and β -hairpins are described, with emphasis on their inter-main chain hydrogen bond patterns. Especially new is the realization that β -hairpins occur in four distinct classes that are of evolutionary and structural significance. Certain of the loop motifs are often found at the ends of particular classes of β -hairpins. Computer-generated pictures allow the three-dimensional hydrogen bond patterns of loops and secondary structural features to be displayed, in simplified form, in entire proteins.

Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of α-helices and antiparallel β-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions

An angle named gamma has been employed to describe the geometry at a hydrogen bond between main-chain atoms of polypeptides. In antiparallel beta-sheet, gamma is normally positive, whereas, in parallel beta-sheet and alpha-helices, it is negative. Although intriguing, no particular explanation has been offered to explain this result. We provide evidence that, in each case, the angular preference maximises the favourable Coulombic interaction between the partial negative charge on the carbonyl oxygen atom and the partial positive charge on the carbonyl carbon atom adjacent to the NH group to which it is hydrogen-bonded. Analyses of helices and beta-sheets in native proteins using Lennard-Jones potentials suggest that these carbonyl-carbonyl interactions are significant components of the attractive forces holding main-chain CONH groups together and are even in some cases larger than the hydrogen bonds themselves. A novel technique for analysing the forces holding together hydrogen-bonding groups in proteins is presented. It can be regarded as a development of the Kabsch and Sander method of calculating the energy of hydrogen bonds between main-chain atoms. In their program, electrostatic interactions are calculated between appropriate pairs of atoms, i.e. NH binding to CO. Instead, in our method, the four N, H, C, and O atoms, in a peptide bond are taken as a unit and the interaction between two NHCO groups calculated. We also use a Lennard-Jones potential, rather than just measuring the Coulombic interaction. With this approach, account is taken of all types of interactions between partially charged atoms, not only the hydrogen bonds.

A comparative analysis of Identity Management Systems

In this paper, we present a comparative analysis of a few popular Identity Management Systems against a set of requirements. Identity Management and Identity Management Systems have gained significant attention in recent years with the proliferation of different web-enabled and e-commerce services leading to an extensive research on the field in the form of several projects producing many standards, prototypes and application models both in the academia and the industry. We have collected and compiled different requirements from different sources to profile an extensive set of requirements that are required for a Privacy-Enhancing Identity Management System and presented them in the form of a taxonomy. Then we have compared some Identity Management Systems against those requirements and presented them in a concise way to help readers find out instantly which systems satisfy what requirements and thus help them to choose the correct one to fit into their own scenarios.

A Comprehensive Study of the Usability of Multiple Graphical Passwords

Recognition-based graphical authentication systems (RBGSs) using images as passwords have been proposed as one potential solution to the need for more usable authentication. The rapid increase in the technologies requiring user authentication has increased the number of passwords that users have to remember. But nearly all prior work with RBGSs has studied the usability of a single password. In this paper, we present the first published comparison of the usability of multiple graphical passwords with four different image types: Mikon, doodle, art and everyday objects (food, buildings, sports etc.). A longitudinal experiment was performed with 100 participants over a period of 8 weeks, to examine the usability performance of each of the image types. The results of the study demonstrate that object images are most usable in the sense of being more memorable and less time-consuming to employ, Mikon images are close behind but doodle and art images are significantly inferior. The results of our study complement cognitive literature on the picture superiority effect, visual search process and nameability of visually complex images.

Passhint: memorable and secure authentication

People find it difficult to remember multiple alphanumeric as well as graphical passwords. We propose a Passhint authentication system (PHAS), where the users have to choose four images and create hints for each one of them in order to register a new password. During authentication, they have to recognize only the target images, which are displayed with their corresponding hints, among collections of 15 decoy images, in a four step process. A usability study was conducted with 40 subjects. They created 1 Mikon, 1 doodle, 1 art and 1 object password and then recalled each password after a period of two weeks (without any practice sessions). The results demonstrated that the memorability of multiple passwords in PHAS is better than in existing Graphical authentication systems (GASs). Although the registration time is high, authentication time for successful attempts is either equivalent to or less than the time reported for previous GASs. A guessability study conducted with the same subjects revealed that art passwords are the least guessable, followed by Mikon, doodle and objects in that order. The results strongly suggest the use of art passwords in PHAS, which would offer usable as well as secure authentication. The preliminary results indicate that PHAS has solved the memorability problem with multiple passwords. We propose two new features that could enhance the security offered by PHAS, but the usability of these features would need to be tested before they could be adopted in practice.

Dynamic Identity Federation Using Security Assertion Markup Language (SAML)

Security Assertion Markup Language (SAML, in short) is one of the most widely used technologies to enable Identity Federation among organisations from different trust domains. Despite its several advantages, one of the key disadvantages of SAML is the mechanism by which an identity federation is established. This mechanism lacks flexibility to create a federation in a dynamic fashion to enable service provisioning (or de-provisioning) in real time. Several different mechanisms to rectify this problem have been proposed. However, most of them require a more elaborate change at the core of the SAML. In this paper we present a simple approach based on an already drafted SAML Profile which requires no change of the SAML, rather it depends on the implementation of SAML. It will allow users to create federations using SAML between two prior unknown organisations in a dynamic fashion. Implicit in each identity federation is the issue of trust. Therefore, we also analyse in detail the trust issues of dynamic federations. Finally, we discuss our implemented proof of concept to elaborate the practicality of our approach.

Measuring the revised guessability of graphical passwords

There is no widely accepted way of measuring the level of security of a recognition-based graphical password against guessing attacks. We aim to address this by examining the influence of predictability of user choice on the guessability and proposing a new measure of guessability. Davis et al. showed that these biases exist for schemes using faces and stories, we support this result and show these biases exist in other recognition-based schemes. In addition, we construct an attack exploiting predictability, which we term “Semantic Ordered Guessing Attack” (SOGA). We then apply this attack to two schemes (the Doodles scheme and a standard recognition-based scheme using photographic images) and report the results. The results show that predictability when users select graphical passwords influence the level of security to a varying degree (dependent on the distractor selection algorithm). The standard passimages scheme show an increase on guessability of up to 18 times more likely than the usual reported guessability, with a similar set up of nine images per screen and four screens, the doodles scheme shows a successful guessing attack is 3.3 times more likely than a random guess. Finally, we present a method of calculating a more accurate guessability value, which we call the revised guessability of a recognition-based scheme. Our conclusion is that to maximise the security of a recognition-based graphical password scheme, we recommend disallowing user choice of images.

A MECHANISM FOR FILTERING DISTRACTORS FOR DOODLE PASSWORDS

Graphical authentication holds some potential as an alternative to the ubiquitous password. Graphical authentication mechanisms typically present users with one or more challenge sets composed of a...