CLIX: a search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure.

A computer algorithm, CLIX, capable of searching a crystallographic data-base of small molecules for candidates which have both steric and chemical likelihood of binding a protein of known three-dimensional structure is presented. The algorithm is a significant advance over previous strategies which consider solely steric or chemical requirements for binding. The algorithm is shown to be capable of predicting the correct binding geometry of sialic acid to a mutant influenza-virus hemagglutinin and of proposing a number of potential new ligands to this protein.     

Fishers' Knowledge of Marine Species Assemblages: Bridging between Scientific and Local Ecological Knowledge in Southeastern Puerto Rico

Increasingly, local ecological knowledge (LEK) held by groups of people engaging directly with their ecosystems for food production is recognized as a valuable tool for understanding environmental change, as well as for ecosystem management and conservation. However, the acceptance of LEK for resource management has been partly hindered by difficulties in translating local knowledge into a form that can be applied directly to Western scientific endeavors. Anthropology's focus on cultural meaning makes its practitioners uniquely qualified to find common ground between different systems of knowledge. Here, I report the use of ethnographic methods to represent Puerto Rican small-scale fishers' knowledge about tropical coastal habitat connectivity and the composition of species assemblages by underwater habitats. These two topics are of current interest for tropical fishery science and their study can benefit from fishers' extensive experience with the coastal environments on which they depend.     

Science in the age of mechanical reproduction: moral and epistemic relations between diagrams and photographs

Sociologists, philosophers and historians of science are gradually recognizing the importance of visual representation. This is part of a more general movement away from a theory-centric view of science and towards an interest in practical aspects of observation and experimentation. Rather than treating science as a matter of demonstrating the logical connection between theoretical and empirical statements, an increasing number of investigations are examining how scientists compose and use diagrams, graphs, photographs, micrographs, maps, charts, and related visual displays. This paper focuses on diagrams in biology, and tries to demonstrate how diagrams are an integral part of the production of scientific knowledge. In order to disclose some of the distinctive practical and analytical uses of diagrams, the paper contrasts the way diagrams and photographs are used in biological texts. Both diagrams and photographs are shown to be “constructions” that separately and together mediate the investigation of scientific phenoman.     

Personal reflections on the nature of intelligence in humans and machines

Computers, the human mind, and social systems have common problems of inadequate memory and insufficient data manipulation speed. In each of these domains, information compression techniques have evolved to reduce storage and processing needs. Among the techniques for information compression, coding of information in procedures stands out as exceptionally powerful. Procedural information coding also gives rise to behavior that may be defined as intelligent. It is found in the human mind, in machines and in social systems. Its use in human thought is aided by language development which promotes regular review of abstract procedures. A practical consequence of better understanding of procedural information coding is the possibility of training people to exhibit greater mental capacity, a controversial possibility. This paper explores the impact of data processing resource limitations, data compression and procedural thinking in men and machines.     

Virtual resource development in the glycosciences

The development of Internet-based virtual resources is a relatively new area of scientific and technical activity that is currently undergoing rapid expansion. Major factors fuelling recent growth include the emergence of multimedia capabilities through the rapid evolution of the World Wide Web, the reduction in cost of high quality personal computers and graphics workstations and the provision of mass-marketed provider services. Prior to 1995 the presence of Internet resources in the glycosciences was virtually non-existent. Existing scientific knowledge was primarily made available on the Net through the provision of databases from gopher and ftp sites. A particular example in the glycosciences is the Carbbank database of biological carbohydrate sequences. We will describe here our efforts in 1994–95 in establishing The Glycoscience Network (TGN, http://bellatrix.pcl.ox.ac.uk/TGN/). These activities included the establishment of a newsgroup, mailing lists, Web resources and the running of the First Electronic Glycoscience Conference (EGC-1, http://bellatrix.pcl.ox.ac.uk/egc/). EGC-1 included many novel initiatives in the glycosciences including electronic posters and papers, a Virtual Conference Centre, a Web-based hyperglossary, Virtual Trade and Employment Centres, refereed electronic publishing, and the creation of a Virtual Reality Gallery. We would like to look towards the near future and discuss several initiatives in virtual resource creation that we believe will have significant scientific impact on the glycosciences including the development of bioinformatics-based servers, sophisticated interactive databases, and videoconferencing. Furthermore, we cherish the belief that these resources will foster international scientific collaboration and progress of an extent never previously possible. Finally, we indulge in speculation and make some suggestions on the form and long-term impact of Glycoscience Virtual Resources. We predict that their development may completely reconstruct the scientific environment that we work in as scientists and we reflect on the probable benefits and pitfalls to be encountered.This paper was presented at the First Electronic Glycoscience Conference (EGCI) on the World Wide Web, September 1995.     

植物资源与化学数据库系统（DPRC）的功能与应用

由中国科学院昆植物研究所和云南省机械研究设计院的植物资源化学数据库系统是一个将植物资源,植物化学成分及化学结构的多种信息、数据和图象融为一体的、开和式多功能软件系统、,包括植资源检索系统、植物化学成分检索系统及天然产物化学结构检索系统等三个子系统。     

物种保护信息管理系统的开发应用

在英文物种、生境和保护区管理系（MASS 3．1）的基础上,研究并改编完成了其中文系统软件包（CMASS 2．0）,并用此中文系统软件包建立了中国自然保护区信息库、中国保护动物信息库、中国濒危动物信息库、中国兽类信息库、中国鸟类信息库,这些库的建立对我国野生动物保护具有重要意义。     

Classification of doubly wound nucleotide binding topologies using automated loop searches

A classification is presented of doubly wound α/β nucleotide binding topologies, whose binding sites are located in the cleft formed by a topological switch point. In particular, the switch point loop nearest the N-terminus is used to identify specific structural classes of binding protein. This yields seven structurally distinct loop conformations, which are subsequently used as motifs for scanning the Protein Data Bank. The searches, which are effective at identifying functional relationships within a large database of structures, reveal a remarkable and previously unnoticed similarity between the coenzyme binding sites of flavodoxin and tryptophan synthetase, even though there is no sequence or topological similarity between them.