FORTE: a profile-profile comparison tool for protein fold recognition

Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods.

To improve the detection of related proteins, it is often useful to include evolutionary information for both the query and target proteins. One method to include this information is by the use of profile-profile alignments, where a profile from the query protein is compared with the profiles from the target proteins. Profile-profile alignments can be implemented in several fundamentally differ...

A COMPARISON BETWEEN THE PROTEIN PROFILE OF lNT ACT AND TWO

DeepSF: deep convolutional neural network for mapping protein sequences to folds

Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a target protein based on the fold of a template protein with known structure, which cannot explain the relationship between sequence and fold. Only a few methods had been developed to class...

SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model

How to recognize the structural fold of a protein is one of the challenges in protein structure prediction. We have developed a series of single (non-consensus) methods (SPARKS, SP(2), SP(3), SP(4)) that are based on weighted matching of two to four sequence and structure-based profiles. There is a robust improvement of the accuracy and sensitivity of fold recognition as the number of matching ...

SP: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model

How to recognize the structural fold of a protein is one of the challenges in protein structure prediction. We have developed a series of single (non-consensus) methods (SPARKS, SP, SP, SP) that are based on weighted matching of two to four sequence and structure-based profiles. There is a robust improvement of the accuracy and sensitivity of fold recognition as the number of matching profiles ...