3658125
PFRES: protein fold classification by using evolutionary information and predicted secondary structure
MOTIVATION
The number of protein families has been estimated to be as small as 1000. Recent study shows that the growth in discovery of novel structures that are deposited into PDB and the related rate of increase of SCOP categories are slowing down. This indicates that the protein structure space will be soon covered and thus we may be able to derive most of remaining structures by using the known folding patterns. Present tertiary structure prediction methods behave well when a homologous structure is predicted, but give poorer results when no homologous templates are available. At the same time, some proteins that share twilight-zone sequence identity can form similar folds. Therefore, determination of structural similarity without sequence similarity would be beneficial for prediction of tertiary structures.


RESULTS
The proposed PFRES method for automated protein fold classification from low identity (<35%) sequences obtains 66.4% and 68.4% accuracy for two test sets, respectively. PFRES obtains 6.3-12.4% higher accuracy than the existing methods. The prediction accuracy of PFRES is shown to be statistically significantly better than the accuracy of competing methods. Our method adopts a carefully designed, ensemble-based classifier, and a novel, compact and custom-designed feature representation that includes nearly 90% less features than the representation of the most accurate competing method (36 versus 283). The proposed representation combines evolutionary information by using the PSI-BLAST profile-based composition vector and information extracted from the secondary structure predicted with PSI-PRED.


AVAILABILITY
The method is freely available from the authors upon request.
15411856
Prediction of the Number of Helices for the Twilight Zone Proteins
Protein structure prediction is one of the core research areas in bioinformatics. This paper addresses the protein secondary structure prediction problem for the twilight zone proteins, which are characterized by low, about 25% homology to the sets of known sequences. The commonly used sequence alignment based algorithms fail to provide accurate prediction for sequences of such low homology, and thus alternative solutions should be sought. We propose a novel method that aims at the prediction of the number of helical structures based on the twilight zone protein sequences. The method is based on a custom designed and compact feature based sequences representation and applies a decision tree prediction algorithm. The performed experimental study shows superiority of the proposed method over three other prediction algorithms and the results provided by YASPIN algorithm, which is a state-of-the-art alignment based secondary structure prediction method designed using low homology sequences
193129
Sequence based residue depth prediction using evolutionary information and predicted secondary structure
BackgroundResidue depth allows determining how deeply a given residue is buried, in contrast to the solvent accessibility that differentiates between buried and solvent-exposed residues. When compared with the solvent accessibility, the depth allows studying deep-level structures and functional sites, and formation of the protein folding nucleus. Accurate prediction of residue depth would provide valuable information for fold recognition, prediction of functional sites, and protein design.ResultsA new method, RDPred, for the real-value depth prediction from protein sequence is proposed. RDPred combines information extracted from the sequence, PSI-BLAST scoring matrices, and secondary structure predicted with PSIPRED. Three-fold/ten-fold cross validation based tests performed on three independent, low-identity datasets show that the distance based depth (computed using MSMS) predicted by RDPred is characterized by 0.67/0.67, 0.66/0.67, and 0.64/0.65 correlation with the actual depth, by the mean absolute errors equal 0.56/0.56, 0.61/0.60, and 0.58/0.57, and by the mean relative errors equal 17.0%/16.9%, 18.2%/18.1%, and 17.7%/17.6%, respectively. The mean absolute and the mean relative errors are shown to be statistically significantly better when compared with a method recently proposed by Yuan and Wang [Proteins 2008; 70:509–516]. The results show that three-fold cross validation underestimates the variability of the prediction quality when compared with the results based on the ten-fold cross validation. We also show that the hydrophilic and flexible residues are predicted more accurately than hydrophobic and rigid residues. Similarly, the charged residues that include Lys, Glu, Asp, and Arg are the most accurately predicted. Our analysis reveals that evolutionary information encoded using PSSM is characterized by stronger correlation with the depth for hydrophilic amino acids (AAs) and aliphatic AAs when compared with hydrophobic AAs and aromatic AAs. Finally, we show that the secondary structure of coils and strands is useful in depth prediction, in contrast to helices that have relatively uniform distribution over the protein depth. Application of the predicted residue depth to prediction of buried/exposed residues shows consistent improvements in detection rates of both buried and exposed residues when compared with the competing method. Finally, we contrasted the prediction performance among distance based (MSMS and DPX) and volume based (SADIC) depth definitions. We found that the distance based indices are harder to predict due to the more complex nature of the corresponding depth profiles.ConclusionThe proposed method, RDPred, provides statistically significantly better predictions of residue depth when compared with the competing method. The predicted depth can be used to provide improved prediction of both buried and exposed residues. The prediction of exposed residues has implications in characterization/prediction of interactions with ligands and other proteins, while the prediction of buried residues could be used in the context of folding predictions and simulations.
41045084
Parallel algorithms of the Purcell method for direct solution of linear systems
In this paper, we first demonstrate that the classical Purcell's vector method when combined with row pivoting yields a consistently small growth factor in comparison to the well-known Gauss elimination method, the Gauss-Jordan method and the Gauss-Huard method with partial pivoting. We then present six parallel algorithms of the Purcell method that may be used for direct solution of linear systems. The algorithms differ in ways of pivoting and load balancing. We recommend algorithms V and VI for their reliability and algorithms III and IV for good load balance if local pivoting is acceptable. Some numerical results are presented.
5116790
Flexible parallelization of fast wavelet transforms
In this paper, we present a new parallel algorithm for fast wavelet transforms (FWT) of a matrix of arbitrary size using any given number of parallel processors. The main idea in achieving the optimal load balancing is through a complexity analysis and flops minimization. This makes parallel implementation of FWT feasible and efficient on distributed memory machines with only a small number of processors and on local area networks. The new algorithm is tested by numerical experiments.
1757195
Combining linear discriminant functions with neural networks for supervised learning
A novel supervised learning method is proposed by combining linear discriminant functions with neural networks. The proposed method results in a tree-structured hybrid architecture. Due to constructive learning, the binary tree hierarchical architecture is automatically generated by a controlled growing process for a specific supervised learning task. Unlike the classic decision tree, the linear discriminant functions are merely employed in the intermediate level of the tree for heuristically partitioning a large and complicated task into several smaller and simpler subtasks in the proposed method. These subtasks are dealt with by component neural networks at the leaves of the tree accordingly. For constructive learning, growing and credit-assignment algorithms are developed to serve for the hybrid architecture. The proposed architecture provides an efficient way to apply existing neural networks (e.g. multi-layered perceptron) for solving a large scale problem. We have already applied the proposed method to a universal approximation problem and several benchmark classification problems in order to evaluate its performance. Simulation results have shown that the proposed method yields better results and faster training in comparison with the multilayered perceptron.
10375004
Optimal Search Model for Combined Strategy in Sequence Alignment
A low power sense amplifier having bit line sensors for sensing the respective voltage levels of a plurality of bit lines, and a latch connected by data lines to the bit lines sensor, for latching the sensed voltage levels. Circuitry of the amplifier prevents formation of a conductive path to ground through both the bit line sensors and the latch when the sensed voltage levels are latched. This provides a sense amplifier which is low in power consumption, while maintaining a relatively high speed, which is particularly useful in CMOS memories.
4925614
Combining Competitive Learning Networks of Various Representations for Sequential Data Clustering
A process for the preparation of oil-soluble Mannich condensation products wherein an amine is prereacted with a sulfonic acid or ammonium sulfonate, and the prereaction product is reacted with an aldehyde and an oxidized olefin polymer.