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We present a novel computational method for Multiple Sequence Alignment (MSA), a fundamental problem in computational biology. In contrast to other known approaches, our method searches for an optimal alignment — structurally and evolutionarily — by inserting or deleting gaps from a set of initial candidates in an efficient manner. Our method called a Universal Partitioning Search (UPS) approach for...
Pairwise protein structure comparison has taken significant scientific research effort in last two decades. Even though it all started with alignment-based comparison methods, recently there are several non-alignment based methods that have shown good potential. One such approach is based on shape descriptors. These methods use histograms or vectors to represent the molecular shapes. They have shown...
Functional region identification is of fundamental importance for protein sequences analysis for a protein family. Such knowledge not only provides a better scientific understanding but also assists drug discovery. Domain annotation is one approach but it needs to leverage existing databases. For de novo discovery, motif discovery locates and aligns locally similar sub-sequences and represents them...
Proteins from the same family have similar functions. Hence, it is important to discover from a protein family conserved sequence patterns with variations to unveil the functionality of a functional domain. Aligned Pattern Clusters (APCs) are knowledge-rich representations comparing with probabilistic models. If significant aligned residue associations (ARAs) were discovered in APCs, they could reveal...
Dihedral angles play a very important role in determining the backbone structure of any protein macromolecule. The backbone structure is associated with protein function. In this work, dihedral angles along with geometric angles have been used as features to represent protein structures. These features are then used to perform protein secondary structural classification.
Co-evolution exists ubiquitously in biological systems. At the molecular level, interacting proteins, such as ligands and their receptors and components in protein complexes, co-evolve to maintain their structural and functional interactions. Many proteins contain multiple functional domains interacting with different partners, making co-evolution of interacting domains occur more prominently. Multiple...
T cells play a critical role in the adaptive immune response. They perform their function by recognizing infected cells presenting peptides on a specialized complex known as the MHC. The recognition process involves binding of the peptide-loaded MHC to the T cell receptor (TCR), a surface molecule comprised of an alpha and a beta chain. A large body of evidence suggests that T cells can respond to...
We have developed a fast, scalable, and purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles. Along the way, we introduce a new torsion angle plot without breaks in continuity while still maintaining traditional torsion angle ranges, to assist in identifying separable regions of torsion angles....
In eukaryotes, protein ubiquitylation is an important type of post-translation modification, in which the ubiquitin conjugates to a substrate protein. To have a better insight of the mechanisms underlying ubiquitylation, a key step is to identify protein ubiquitylation sites. Many existing computational methods are based on feature engineering, which may lead to biased and incomplete features. Deep...
Database search is the main approach for identifying proteoforms using top-down tandem mass spectra. However, it is extremely slow to align a query spectrum against all protein sequences in a large database when the target proteoform that produced the spectrum contains post-translational modifications and/or mutations. As a result, efficient and sensitive protein sequence filtering algorithms are...
Antimicrobial peptides are short amino acid sequences with antibacterial, antifungal, and antiviral properties. Antibacterial peptides have the possibility to form a new class of antibiotics to aid in combating bacterial antibiotic resistance. Most machine learning methodologies applied to the task of identifying antimicrobial peptides have applied features representing the presence or absence of...
Sequence comparison is a fundamental task in computational biology, traditionally dominated by alignment-based methods such as the Smith-Waterman and Needleman-Wunsch algorithms, or by alignment based heuristics such as BLAST, the ubiquitous Basic Local Alignment Search Tool. For more than a decade researchers have examined a range of alignment-free alternatives to these approaches, citing concerns...
The fundamental principle of the evolution of all material and element base of neural computing, in particular, is the preservation of the singularity of the mechanisms of its synthesis and functioning shown. The development of control algorithms and self-organization lies in the field of compatibility to singular processes and structures, where the neural associative computing has apparent advantages...
A protein is a long one-dimensional amino acid sequence. Some subsequences of this sequence are given names and β-strand in one such subsequence. β-strands are very common and two or more such strands within one protein can form a β-sheet in the secondary structure of proteins. In its natural form, a protein is a three-dimensional entity composed of β-sheets, α-helices, and other types of substructures...
In this paper, a long sequence feature extraction method (LSFE) is proposed for protein secondary structure prediction. The proposed method is based on deep learning architecture which is mainly composed of three-layers: sparse auto-encoder, convolution feature extraction layer, and the softmax classifier. PSSM (position-specific scoring matrix) is used as the raw sequence representation. Two groups...
This article presents a new SVM classifier for the prediction of the extended early-stage (ES) protein structures. The classifier is based on physicochemical features and position-specific scoring matrix (PSSM). Experiments have shown that prediction results for specific classes are significantly better than those already obtained.
Proteins are among the most fundamental molecules in living organisms. Investigation and comparison of their three-dimensional structure is an important task in structural bioinformatics as global and local similarities can be of functional importance. Structure alignment and comparison is computationally intensive, so typically a number of simplifications are used for practical reasons. However,...
The purpose was to use mathematical modeling calculate the fingerprints, quantitative research on traditional Chinese medicine information. We gave a new way to establish four common diseases CGR fingerprint sequence diagram, then gave their usage degree of the synonymous fingerprint sequence defined QRSFU. The preference characteristics of four common disease fingerprint sequences for synonymous...
The current literature review provides an analysis of fundamental studies on the −2proPSA index and prostate health index PHI and determination of their role in patients with prostate cancer. The authors revealed the basic aspects of the studied markers such as the improvement of prostate cancer detection, increase of specificity and reduction of unnecessary biopsies, identification of aggressive...
In order to understand the structure and folding of proteins, Hydrophobic-Polar (HP) model on 2D square lattice is one of the most explored models but parity problem of square lattice make it inefficient for biological applications. This work is dedicated to solve parity issues in 2D square lattice model. This work proposes a revised energy function and presents a case study for protein structure...
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