منابع مشابه
Improving fold recognition without folds.
The most reliable way to align two proteins of unknown structure is through sequence-profile and profile-profile alignment methods. If the structure for one of the two is known, fold recognition methods outperform purely sequence-based alignments. Here, we introduced a novel method that aligns generalised sequence and predicted structure profiles. Using predicted 1D structure (secondary structu...
متن کاملProtein fold recognition without Boltzmann statistics or explicit physical basis.
We present a fast method for finding optimal parameters for a low-resolution (threading) force field intended to distinguish correct from incorrect folds for a given protein sequence. In contrast to other methods, the parameterization uses information from >10(7) misfolded structures as well as a set of native sequence-structure pairs. In addition to testing the resulting force field's performa...
متن کاملFold recognition using predicted secondary structure sequences and hidden Markov models of protein folds.
We present an analysis of the blind predictions submitted to the fold recognition category for the second meeting on the Critical Assessment of techniques for protein Structure Prediction. Our method achieves fold recognition from predicted secondary structure sequences using hidden Markov models (HMMs) of protein folds. HMMs are trained only with experimentally derived secondary structure sequ...
متن کاملPredicting Protein Folds with Fold-Specific PSSM Libraries
Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies. Herein, we outline an effective method for fold recognition using sets of PSSMs, each of which is constructed for different protein folds. Our analyses demonstrate that FSL (Fold-specific Position Specific Scoring Matrix Libraries) can predict/relate structures given only their amino acid seque...
متن کاملConfidence Measures for Fold Recognition
It is a standard procedure to compare new amino acid sequences to databases of proteins that have been studied already in order to find similarities in structure and function. This comparison can be sequence–sequence or sequence– structure based. In order to compare, an alignment is performed of the target protein sequence (whose structure we are searching) with a template protein (whose struct...
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ژورنال
عنوان ژورنال: Protein Science
سال: 2002
ISSN: 0961-8368,1469-896X
DOI: 10.1110/ps.3590102