![]() 281 565–577Ĭamproux A C, Brevern A G, Hazout S and Tufféry P 2001 Exploring the use of a structural alphabet for structural prediction of protein loops Theor. Sensitivity Study And Improvements Of The Training in IEEE Workshop on Neural Networks for Signal Processing (Toulouse, France) pp 53–72īenros C, de Brevern A G and Hazout S 2004 Predicting Local Structural Candidates from Sequence by the “Hybrid Protein Model” Approach in 12th Intelligent Systems for Molecular Biology (ISMB) / 3rd the European Conference on Computational Biology (ECCB), Glasgowīystroff C and Baker D 1998 Prediction of local structure in proteins using a library of sequence-structure motifs J. ![]() 215 403–410īairoch A, Boeckmann B, Ferro S and Gasteiger E 2004 Swiss-Prot: juggling between evolution and stability Brief Bioinform 5 39–55īenros C, de Brevern A G, Etchebest C and Hazout S 2006 Assessign a novel approach for predicting local 3D protein structures from sequence Proteins 62 865–880īenros, C, de Brevern A G and Hazout S 2003 Hybrid Protein Model (HPM): A Method For Building A Library Of Overlapping Local Structural Prototypes. 33 W44–W49Īltschul S.F, Gish W, Miller W, Myers E W and Lipman D J 1990 Basic local alignment search tool J. 2005 RPBS: a web resource for structural bioinformatics Nucleic Acids Res. In a second step, the sequence-structure relationship is optimized, the prediction accuracy reaches 43.6%.Īlexandrov N and Shindyalov I 2003 PDP: protein domain parser Bioinformatics 19 429–430Īlland C, Moreews F, Boens D, Carpentier M, Chiusa S, Lonquety M, Renault N, Wong Y, Cantalloube H, Chomilier J et al. The pinning strategy simply applied to the SWs increases the prediction accuracy to 39.9%. Starting from an initial prediction rate of 34.4%, the use of the SWs instead of the PBs allows a gain of 4.5%. It starts from the most probable SW and is then extended with overlapping SWs. Its goal is to define highly probable successions of PBs. In this study, we propose a new method called “pinning strategy” that used this specific feature to predict long protein fragments. PBs are highly conditioned by the presence of a limited number of transitions between them. The 72 most frequent series of 5 consecutive PBs, called structural words (SWs) are able to cover more than 90% of the 3D structures. ![]() It allows an efficient approximation of the 3D protein structures and a correct prediction of the local structure. Our structural alphabet is composed of 16 small protein fragments of 5 C α in length, called protein blocks (PBs). ![]() The description of protein 3D structures can be performed through a library of 3D fragments, named a structural alphabet. ![]()
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