Peter R. Sibbald

The P-loop — a common motif in ATP- and GTP-binding proteins

Many ATP- and GTP-binding proteins have a phosphate-binding loop (P-loop), the primary structure of which typically consists of a glycine-rich sequence followed by a conserved lysine and a serine or threonine. The three-dimensional structures of several ATP- and GTP-binding proteins containing P-loops have now been solved. In this review current knowledge of P-loops is discussed with the additional aim of illustrating the fascinating relationship between protein sequence, structure and function.

Weighting aligned protein or nucleic acid sequences to correct for unequal representation

Aligned sequences from the same family (e.g. the haemoglobins) are seldom representative of the entire family. This is because (1) the sequence databases are heavily skewed toward a small number of organisms and (2) only a minute fraction of all the different family members have been sequenced. For many applications, such as using alignments or profiles to perform database searches for distantly related family members, such unequal representation requires correction. An algorithm to perform appropriate weighting of individual sequences is presented along with examples illustrating its efficacy.

Identification of proteins in sequence databases from amino acid composition data

Having obtained the amino acid composition of a protein, chemists and molecular biologists may wish to identify the protein from this data alone. In general such data will have errors associated with them and the length of the protein may be known only approximately or not at all. In this paper a method is described which enables searching of protein sequence databases for sequences or fragments of sequences which have a composition similar to the one being sought. Such searches are generally quite discriminating as shown by the examples provided. This method has been implemented as part of the computer program Scrutineer and is being freely distributed. It is simple to use.

Scrutineer: a computer program that flexibly seeks and describes motifs and profiles in protein sequence databases

Scrutineer is an interactive, user-friendly program designed to search for motifs, patterns and profiles in the Swissprot, Protein Identification Resource (PIR) or SeqDb protein sequence databases. Basic capabilities include (i) searches for strings of amino acids with multiple choices at a given position; (ii) searches for strings including variable-length segments and delocalized constraints; (iii) searches over subsets of a database or particular regions within each sequence (e.g. N-terminal one-third); (iv) searches involving secondary structure predictions, physicochemical characteristics, and the like; and (v) searches using aligned sequences as targets with various optional weighting schemes. The various search criteria and hits can be combined and complex targets located. Once the data are loaded into virtual memory, all occurrences in PIR release 22.0 (3.7 x 10(6) amino acids) of a given short string of amino acids (e.g. a hexamer) are found in approximately 36 s. Scrutineer can also describe the entire database, user-specified hits, user-defined regions of sequence and all hits. The source code and accompanying manual are being freely distributed.

Automated protein sequence pattern handling and PROSITE searching

The protein sequence searching program Scrutineer has been modified to search for targets from a file. We are distributing a reformatted file of PROSITES which can be read by Scrutineer. In addition, Scrutineer still accepts targets typed in interactively but can now write them out in the format required as input. Since the input format is the same as the output format, target management and re-use is simple.

Overseer : a nucleotide sequence searching tool

Overseer is a computer program that searches databases of nucleic acid sequences for objects of interest to the user. Such objects may consist of any number of simpler building blocks such as repeats, palindromes or stem-loops, strings of particular bases with or without mismatches, etc. Written in standard Pascal, this program runs under Unix and VMS and should also run under other operating systems. A simple interface allows the user to generate interactively a file containing a description of the target to be found. The searching program runs non-interactively, processing the information from the file and searching the sequences. The results are output to a file. Search capabilities are quite flexible and the code is designed to be modified. Since the framework of the program is simple, adding new modules to search for new target types as the need arises is possible.

Integration of molecular biology data collections using object oriented databases and programming

Molecular biology is the study of the molecules that make up living things. These molecules include DNA, RNA, proteins, carbohydrates, lipids etc. Biologists seek to understand the function, structure, location, synthesis, regulation, dynamics, interaction and origin of these molecules. Such a discipline is motivated not only by practical problems in fields like medicine and biotechnology but also by curiosity about life itself. There are a number of data collections in molecular biology that would be much more powerful if they could be used in concert. Our ultimate aim is to be able to make arbitrarily complex queries across these data collections. Ultimately the computer naive user who is an expert biologist should be able to readily make any query without having to know where the data reside, how they are accessed or what programs are used In other words, the biologist should be able to work in an extremely high level way.

SCRUTINEER: a Program to Explore and Evaluate Protein Sequence Patterns in Databases

SCRUTINEER is a computer program designed to search protein sequence databases for features of interest to molecular biologists. The program has been described in detail elsewhere (Sibbald and Argos, 1990a); only a brief description is given here. As originally conceived, the program was required to effect interactive exploration of protein sequences and describe features of interest once located. To enhance portability of the program, it was written in standard Pascal. SCRUTINEER only works with the sequence part of databases and not the annotation since many other programs already search the latter [e.g. PSQ (Sidman et al, 1988), GCG (Devereux et al, 1984)].