The characterization of interactions in protein–ligand complexes is essential for research in structural bioinformatics, drug discovery and biology. However, comprehensive tools are not freely available to the research community. Here, we present the protein–ligand interaction profiler (PLIP), a novel web service for fully automated detection and visualization of relevant non-covalent protein–ligand contacts in 3D structures, freely available at . The input is either a Protein Data Bank structure, a protein or ligand name, or a custom protein–ligand complex (e.g. from docking). In contrast to other tools, the rule-based PLIP algorithm does not require any structure preparation. It returns a list of detected interactions on single atom level, covering seven interaction types (hydrogen bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt bridges, water bridges and halogen bonds). PLIP stands out by offering publication-ready images, PyMOL session files to generate custom images and parsable result files to facilitate successive data processing. The full python source code is available for download on the website. PLIP's command-line mode allows for high-throughput interaction profiling.

R o g e r M . N e e d h a m a n d M i c h a e l D . S c h r o e d e r X e r o x P a l o A l t o R e s e a r c h C e n t e r Use of encryption to achieve authenticated communication in computer networks is discussed. Example protocols are presented for the establishment of authenticated connections, for the management of authenticated mail, and for signature verification and document integrity guarantee. Both conventional and public-key encryption algorithms are considered as the basis for protocols.Key Words and Phrases: encryption, security, authentication, networks, protocols, public-key cryptosystems, data encryption standard CR Categories: 3.81, 4.31, 4.35 IntroductionIn the context of secure computer communications, authentication means verifying the identity of the communicating principals to one another. A network in which a large number of computers communicate may have no central machine or system that contains authorPermission to copy without fee all or part of this material is granted provided that the copies are not made or distributed for direct commercial advantage, the ACM copyright notice and the title of the publication and its date appear, and notice is given that copying is by permission of the Association for Computing Machinery. To copy otherwise, or to republish, requires a fee and/or specific permission. 993itative descriptions of the connected computers, of the purposes for which they are used, or of the individuals who use them. We present protocols for decentralized authentication in such a network that are integrated with the allied subject of naming. There is minimal reliance on network-wide services; in particular there is no reliance on a single network clock or a single network name management authority.Three functions are discussed:(1) Establishment of authenticated interactive communication between two principals on different machines. By interactive communication we mean a series of messages in either direction, typically each in response to a previous one.(2) Authenticated one-way communication, such as is found in mail systems, where it is impossible to require protocol exchanges between the sender and the recipient while sending an item, since there can be no guarantee that sender and recipient are simultaneously available.(3) Signed communication, in which the origin of a communication and the integrity of the content can be authenticated to a third party.Secure communication in physically vulnerable networks depends upon encryption of material passed between machines. We assume that it is feasible for each computer in the network to encrypt and decrypt material efficiently with arbitrary keys, and that these keys are not readily discoverable by exhaustive search or cryptanalysis. We consider both conventional encryption algorithms and public-key encryption algorithms as a basis for the protocols presented.We assume that an intruder can interpose a computer in all communication paths, and thus can alter or copy parts of messages, replay messages, or emit false material. Whi...

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With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules is gaining importance. PLIP, the protein–ligand interaction profiler, detects and visualises these interactions and provides data in formats suitable for further processing. PLIP has proven very successful in applications ranging from the characterisation of docking experiments to the assessment of novel ligand–protein complexes. Besides ligand–protein interactions, interactions with DNA and RNA play a vital role in many applications, such as drugs targeting DNA or RNA-binding proteins. To date, over 7% of all 3D structures in the Protein Data Bank include DNA or RNA. Therefore, we extended PLIP to encompass these important molecules. We demonstrate the power of this extension with examples of a cancer drug binding to a DNA target, and an RNA–protein complex central to a neurological disease. PLIP is available online at https://plip-tool.biotec.tu-dresden.de and as open source code. So far, the engine has served over a million queries and the source code has been downloaded several thousand times.

Autonet is a self-configuring local area network composed of switches interconnected by 100 Mbit/second, full-duplex, point-to-point links. The switches contain 12 ports that are internally connected by a full crossbar. Switches use cut-through to achieve a packet forwarding latency as low as 2 microseconds per switch. Any switch port can be cabled to any other switch port or to a host network controller.A processor in each switch monitors the network's physical configuration. A distributed algorithm running on the switch processors computes the routes packets are to follow and fills in the packet forwarding table in each switch. This algorithm automatically recalculates the forwarding tables to incorporate repaired or new links and switches, and to bypass links and switches that have failed or been removed. Host network controllers have alternate ports to the network and fail over if the active port stops working.With Autonet, distinct paths through the set of network links can carry packets in parallel. Thus, in a suitable physical configuration, many pairs of hosts can communicate simultaneously at full link bandwidth. The aggregate bandwidth of an Autonet can be increased by adding more links and switches. Each switch can handle up to 2 million packets/second. Coaxial links can span 100 meters and fiber links can span two kilometers.A 30-switch network with more than 100 hosts is the service network for