AlignHUSH: alignment of HMMs using structure and hydrophobicity information.

Background: Sensitive remote homology detection and accurate alignments especially in the midnight zone of sequence similarity are needed for better function annotation and structural modeling of proteins. An algorithm, AlignHUSH for HMM-HMM alignment has been developed which is capable of recognizing distantly related domain families The method uses structural information, in the form of predicted secondary structure probabilities, and hydrophobicity of amino acids to align HMMs of two sets of aligned sequences. The effect of using adjoining column(s) information has also been investigated and is found to increase the sensitivity of HMM-HMM alignments and remote homology detection.

Prediction of protein-protein interactions between human host and a pathogen and its application to three pathogenic bacteria.

Molecular understanding of disease processes can be accelerated if all interactions between the host and pathogen are known. The unavailability of experimental methods for large-scale detection of interactions across host and pathogen organisms hinders this process. Here we apply a simple method to predict protein-protein interactions across a host and pathogen organisms.

Prediction of protein-protein interactions between Helicobacter pylori and a human host.

A lack of information on protein-protein interactions at the host-pathogen interface is impeding the understanding of the pathogenesis process. A recently developed, homology search-based method to predict protein-protein interactions is applied to the gastric pathogen, Helicobacter pylori to predict the interactions between proteins of H. pylori and human proteins in vitro.

Evolutionary divergence of Plasmodium falciparum: sequences, protein-protein interactions, pathways and processes.

In this article we review the organism-wide biological data available for Plasmodium falciparum (P. falciparum), a malarial parasite, in relation to the data available for other organisms. We provide comparisons at different levels such as amino acid sequences of proteins encoded in the genomes, protein-protein interaction features, metabolic and signaling pathways and processes.

A data integration approach to predict host-pathogen protein-protein interactions: application to recognize protein interactions between human and a malarial parasite.

Lack of large-scale efforts aimed at recognizing interactions between host and pathogens limits our understanding of many diseases. We present a simple and generally applicable bioinformatics approach for the analysis of possible interactions between the proteins of a parasite, Plasmodium falciparum, and human host. In the first step, the physically compatible interactions between the parasite and human proteins are recognized using homology detection.

Strategies for the effective identification of remotely related sequences in multiple PSSM search approach.

Searches using position specific scoring matrices (PSSMs) have been commonly used in remote homology detection procedures such as PSI-BLAST and RPS-BLAST. A PSSM is generated typically using one of the sequences of a family as the reference sequence. In the case of PSI-BLAST searches the reference sequence is same as the query.

MulPSSM: a database of multiple position-specific scoring matrices of protein domain families.

Representation of multiple sequence alignments of protein families in terms of position-specific scoring matrices (PSSMs) is commonly used in the detection of remote homologues. A PSSM is generated with respect to one of the sequences involved in the multiple sequence alignment as a reference. We have shown recently that the use of multiple PSSMs corresponding to an alignment, with several sequences in the family used as reference, improves the sensitivity of the remote homology detection dramatically.

Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

Background: A polypeptide chain of a protein-protein complex is said to be obligatory if it is bound to another chain throughout its functional lifetime. Such a chain might not adopt the native fold in the unbound form. A non-obligatory polypeptide chain associates with another chain and dissociates upon molecular stimulus.

A graph spectral analysis of the structural similarity network of protein chains.

We present a simple method for the analysis of large networks based on their graph spectral properties. One of the advantages of this method is that it uses a single numerical computation to identify subclusters in a connected graph, which can significantly simplify the complexity involved in analyzing large graphs. This is illustrated using a network of protein chains constructed on the basis of their structural similarities.

PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families.

PROtein Domain Organization and Comparison (PRODOC) comprises several programs that enable convenient comparison of proteins as a sequence of domains. The in-built dataset currently consists of approximately 698 000 proteins from 192 organisms with complete genomic data, and all the SWISSPROT proteins obtained from the Pfam database. All the entries in PRODOC are represented as a sequence of functional domains, assigned using hidden Markov models, instead of as a sequence of amino acids.