Challenges and other linked features in promoting open access to bioinformation literature over about 2 decades.

Open access to known literature is critical for creating a harmonious society across continents on planet earth. However, this objective is not simple. Therefore, it is of interest to document the challenges and linked features in promoting open access to bioinformation literature over about 2 decades.

From Anna University to America and to Agriculture.

Anna University (AU) is an awesome alma mater for attracting the attention of the invincible through awareness from education. It is a place with a plan for preparing a palace in a person's life. It is an avenue for America through adequate cGPA and Advanced GRE (AGRE) with good TOEFL score.

Pointless pondering on predatory publications.

It is a pointless pondering (thinking) on predatory (meaning greedy) publications (meaning journals) while practicing publishing through freedom of expression and or the Press where applicable. It should be noted that a weak publication will vanish (disappear) itself in an open access publishing model where contents are made available for free on the WWW. The fundamental question in this context is the definition of host (congregation) and predator (intruder).

Science for service in a society is the success story of scientists with serenity.

Available data on science is constantly gleaned for gathering valuable information to create concise yet precise knowledge on specific subjects (especially, the biology oriented agriculture and biomedicine) for service in the society. These sacrifices surmounts as success stories for scientists worldwide. Data in the form of known literature plays a radical role in serving the society with improved infrastructure and facilities making associated resources available, accessible and affordable.

Biotechnology, Bioinformatics and Bioinformation in an Autobiography.

Science is observation. Application of Science is engineering. A 0% error is desired in Science, while a 25% error is usually allowed in Engineering.

Small protein-protein interfaces rich in electrostatic are often linked to regulatory function.

Protein-protein interaction (PPI) is critical for several biological functions in living cells through the formation of an interface. Therefore, it is of interest to characterize protein-protein interfaces using an updated non-redundant structural dataset of 2557 homo (identical subunits) and 393 hetero (different subunits) dimer protein complexes determined by X-ray crystallography. We analyzed the interfaces using van der Waals (vdW), hydrogen bonding and electrostatic energies.

Protein-protein interfaces are vdW dominant with selective H-bonds and (or) electrostatics towards broad functional specificity.

Several catalysis, cellular regulation, immune function, cell wall assembly, transport, signaling and inhibition occur through Protein- Protein Interactions (PPI). This is possible with the formation of specific yet stable protein-protein interfaces. Therefore, it is of interest to understand its molecular principles using structural data in relation to known function.

Insights from the structural analysis of protein heterodimer interfaces.

Protein heterodimer complexes are often involved in catalysis, regulation, assembly, immunity and inhibition. This involves the formation of stable interfaces between the interacting partners. Hence, it is of interest to describe heterodimer interfaces using known structural complexes.

Structural inferences for Cholera toxin mutations in Vibrio cholerae.

Cholera is a global disease that has persisted for millennia. The cholera toxin (CT) from Vibrio cholerae is responsible for the clinical symptoms of cholera. This toxin is a hetero-hexamer (AB(5)) complex consisting of a subunit A (CTA) with a pentamer (B(5)) of subunit B (CTB).

Interaction modes at protein hetero-dimer interfaces.

Hetero dimer (different monomers) interfaces are involved in catalysis and regulation through the formation of interface active sites. This is critical in cell and molecular biology events. The physical and chemical factors determining the formation of the interface active sites is often large in numbers.

A HLA-DRB supertype chart with potential overlapping peptide binding function.

HLA-DRB alleles are class II alleles that are associated with CD4+ T-cell immune response. DRB alleles are polymorphic and currently there are about 622 named in the IMGT/HLA sequence database. Each allele binds short peptides with high sensitivity and specificity.

Structural features for homodimer folding mechanism.

The homodimers have essential role in catalysis and regulation. The homodimer folding mechanism through 2-state without stable intermediate (2S), 3-state with monomer intermediate (3SMI) and 3-state with dimer intermediate (3SDI) is fascinating. 23MI and 3SDI constitute 3-state (3S).

Class II HLA-peptide binding prediction using structural principles.

The precise prediction of class II human leukocyte antigen (HLA) peptide binding finds application in epitope design for the development of vaccines and diagnostics of diseases associated with CD4+ T-cellular immunity. HLA II binding peptides have an extended conformation at the binding groove unlike class I. This increases peptide binding combinations of varying length at the groove, having an eventual effect in the host immune response to infectious agents.

A decision tree model for the prediction of homodimer folding mechanism.

The formation of protein homodimer complexes for molecular catalysis and regulation is fascinating. The homodimer formation through 2S (2 state), 3SMI (3 state with monomer intermediate) and 3SDI (3 state with dimer intermediate) folding mechanism is known for 47 homodimer structures. Our dataset of forty-seven homodimers consists of twenty-eight 2S, twelve 3SMI and seven 3SDI.

Types of interfaces for homodimer folding and binding.

Homodimers have a role in catalysis and regulation through the formation of stable interfaces. These interfaces are formed through different folding mechanisms such as 2-state without stable intermediate (2S), 3-state with monomer intermediate (3SMI) and 3-state with dimer intermediate (3SDI). Therefore, it is of interest to understand folding mechanism using structural features at the interfaces.

HLA-peptide binding prediction using structural and modeling principles.

Short peptides binding to specific human leukocyte antigen (HLA) alleles elicit immune response. These candidate peptides have potential utility in peptide vaccine design and development. The binding of peptides to allele-specific HLA molecule is estimated using competitive binding assay and biochemical binding constants.

Grouping of class I HLA alleles using electrostatic distribution maps of the peptide binding grooves.

Human leukocyte antigen (HLA) molecules involved in immune function by binding to short peptides (8-20 residues) have different sequences in different individuals belonging to distinct ethnic population. Hence, the peptide-binding function of HLA alleles is specific. Class I HLA alleles (alternative forms of a gene) are associated with CD8+ T cells, and their allele-specific sequence information is available at the IMGT/HLA database.

Structural basis for HLA-A2 supertypes.

The human leukocyte antigen (HLA) alleles are extremely polymorphic among ethnic population, and the peptide-binding specificity varies for different alleles in a combinatorial manner. However, it has been suggested that majority of alleles can be covered within few HLA supertypes, where different members of a supertype bind similar peptides, yet exhibiting distinct repertoires. Nonetheless, the structural basis for HLA supertype-like function is not clearly known.

Insight into gene fusion from molecular dynamics simulation of fused and un-fused IGPS (Imidazole Glycerol Phosphate Synthetase).

Gene fusion produces proteins with novel structural architectures during evolution. Recent comparative genome analysis shows several cases of fusion/fission across distant phylogeny. However, the selection forces driving gene fusion are not fully understood due to the lack of structural, dynamics and kinetics data.

Identification of hot spot residues at protein-protein interface.

It is known that binding free energy of protein-protein interaction is mainly contributed by hot spot (high energy) interface residues. Here, we investigate the characteristics of hot spots by examining inter-atomic sidechain-sidechain interactions using a dataset of 296 alanine-mutated interface residues. Results show that hot spots participate in strong and energetically favorable sidechain-sidechain interactions.

Bioinformatics models in drug abuse and Neuro-AIDS: Using and developing databases.

The magnitude of the problems of drug abuse and Neuro-AIDS warrants the development of novel approaches for testing hypotheses in diagnosis and treatment ranging from cell culture models to developing databases. In this study, cultured neurons were treated with/without HIV-TAT, ENV, or cocaine in a 2x2x2 expression study design. RNA was purified, labeled, and expression data were produced and analyzed using ANOVA.

Structural features differentiate the mechanisms between 2S (2 state) and 3S (3 state) folding homodimers.

The formation of homodimer complexes for interface stability, catalysis and regulation is intriguing. The mechanisms of homodimer complexations are even more interesting. Some homodimers form without intermediates (two-state (2S)) and others through the formation of stable intermediates (three-state (3S)).

Protein subunit interfaces: heterodimers versus homodimers.

Protein dimers are either homodimers (complexation of identical monomers) or heterodimers (complexation of non-identical monomers). These dimers are common in catalysis and regulation. However, the molecular principles of protein dimer interactions are difficult to understand mainly due to the geometrical and chemical characteristics of proteins.

T-Epitope Designer: A HLA-peptide binding prediction server.

Unlabelled: The current challenge in synthetic vaccine design is the development of a methodology to identify and test short antigen peptides as potential T-cell epitopes. Recently, we described a HLA-peptide binding model (using structural properties) capable of predicting peptides binding to any HLA allele. Consequently, we have developed a web server named T-EPITOPE DESIGNER to facilitate HLA-peptide binding prediction.