PROTEIN-STRUCTURE PREDICTION - RECOGNITION OF PRIMARY, SECONDARY, ANDTERTIARY STRUCTURAL FEATURES FROM AMINO-ACID-SEQUENCE

This review attempts a critical stock-taking of the current state of t he science aimed at predicting structural features of proteins from th eir amino acid sequences. At the primary structure level, methods are considered for detection of remotely related sequences and for recogni zing amino acid patterns to predict posttranslational modifications an d binding sites. The techniques involving secondary structural feature s include prediction of secondary structure, membrane-spanning regions , and secondary structural class. At the tertiary structural level, me thods for threading a sequence into a mainchain fold, homology modelin g and assigning sequences to protein families with similar folds are d iscussed. A literature analysis suggests that, to date, threading tech niques are not able to show their superiority over sequence pattern re cognition methods. Recent progress in the state of ab initio structure calculation is reviewed in detail. The analysis shows that many struc tural features can be predicted from the amino acid sequence much bett er than just a few years ago and with attendant utility in experimenta l research. Best prediction can be achieved for new protein sequences that can be assigned to well-studied protein families. For single sequ ences without homologues, the folding problem has not yet been solved.