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S E Brenner

Publications and source records attributed to S E Brenner.

11 recordsLinked to original sources
PubMed1995

Classification of multi-helical DNA-binding domains and application to predict the DBD structures of sigma factor, LysR, OmpR/PhoB, CENP-B, Rapl, and Xy1S/Ada/AraC.

We have systematically compared structures of multi-helical DNA-binding domains (DBDs) which have been determined by crystallography or NMR spectroscopy. All the known multi-helical DBDs are very similar. The core of these structures consists of two alpha-helices in the helix-turn-helix combination, associated with one or two other helices. The structures can be classified according to either additional structural compositions or the configuration of the helices. Many DBDs, whose structures are currently unknown, have sequences which resemble those of known structures, permitting outlines of the new structures to be predicted.

Amino Acid Sequence↗
PubMed1995

SCOP: a structural classification of proteins database for the investigation of sequences and structures.

To facilitate understanding of, and access to, the information available for protein structures, we have constructed the Structural Classification of Proteins (scop) database. This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure. It also provides for each entry links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references. Two search facilities are available. The homology search permits users to enter a sequence and obtain a list of any structures to which it has significant levels of sequence similarity. The key word search finds, for a word entered by the user, matches from both the text of the scop database and the headers of Brookhaven Protein Databank structure files. The database is freely accessible on World Wide Web (WWW) with an entry point to URL http: parallel scop.mrc-lmb.cam.ac.uk magnitude of scop.

Amino Acid Sequence↗
PubMed1995

A specification for defining and annotating regions of macromolecular structures.

We present a program- and machine-independent standard for annotating macromolecular structures. Data encoded by this specification may be used for communicating information about structures and for exchanging it between different computer systems. The format consists of a set of ASN.1 objects which are mechanically straightforward to parse, but are also easy for humans to create and understand. It differs from all other related standards in that it specifies how a molecule should be displayed without requiring a custom format for the coordinate data.

Amino Acid Sequence↗
PubMed1994

A quantitative methodology for the de novo design of proteins.

We have developed a general quantitative methodology for designing proteins de novo, which automatically produces sequences for any given plausible protein structure. The method incorporates statistical information, a theoretical description of protein structure, and motifs described in the literature. A model system embodying a portion of the quantitative methodology has been used to design many protein sequences for the phage 434 Cro and fibronectin type III domain folds, as well as several other structures. Residue sequences selected by this prototype share no significant identity with any natural protein. Nonetheless, 3-dimensional models of the designed sequences appear generally plausible. When examined using secondary structure prediction methods and profile analysis, the designed sequences generally score considerably better than the natural ones. The designed sequences are also in reasonable agreement with a sequence template. This quantitative methodology is likely to be capable of successfully designing new proteins and yielding fundamental insights about the determinants of protein structure.

Amino Acid Sequence↗
PubMed1994

Protein design by optimization of a sequence-structure quality function.

An automated procedure for protein design by optimization of a sequence-structure quality has been developed. The method selects a statistically optimal sequence for a particular structure, on the assumption that such a protein will adopt the desired structure. We present two optimization algorithms: one provides an exact optimization while the other uses a combinatorial technique for comparatively rapid results. Both are suitable for massively parallel computers. A prototype system was used to design sequences which should adopt the four-helix bundle conformation of myohemerythrin. These appear satisfactory to secondary structure and profile analysis. Detailed inspection reveals that the sequences are generally plausible but, as expected, lack some specific structural features. The design parameters provide some insight into the general determinants of protein structure.

Algorithms↗