Structural Biology

Biomolecules are too small to view even by the advanced microscopes. Structure probing biochemical techniques determine these biomolecular structures in vast numbers of the same identical molecules at once. Scientists use them to study the "native states" of biomolecules. Few of the best methods determining the structures include X-ray crystallography, Cryo-Electron Microscopy and Nuclear Magnetic Resonance.

• Mass spectrometry
• Macromolecular crystallography Proteolysis
• Nuclear magnetic resonance spectroscopy of proteins (NMR) 
• Electron paramagnetic resonance (EPR)
• Cryo-electron microscopy (cryo-EM)
• Multiangle light scattering
• Small angle scattering
• Ultrafast laser spectroscopy
• Dual-polarization interferometry and circular dichroism

3D Structure Determination summarizes the protein structural predictions, as a main scope for understanding and manipulating of its biochemical and cellular functions using the software tools of modern technology. This major aspect is based on computational aspects used in Bioinformatics and chemistry. Computational prediction methods, as Ab initio fragment assembly, advanced fold recognition, composite approaches, and molecular docking are explicitly applied to extend the deeper study of protein structures.

• Cryo-Electron Microscopy 
• Dual polarization interferometry
• Nuclear Magnetic Resonances
• X-ray crystallography
• Crystallography
• Powder diffractometry
• Mass spectroscopy
• Multi-angle light scattering
• Ultra-fast laser spectroscopy

With the increase in studies of biosciences and urge of emerging computational and experimental techniques, the application of the computational tools and expertise in the biophysics has led the way for emerging computer programming for the immense biological studies. Computer programs predict atomic, molecular properties and reaction paths for chemical reactions of biomolecules. Structural genomics emphasizes high throughput of every protein encoded by the genome determining protein structures. These methods help in scrutinizing the protein structures which are cost effective and time conservative.

• Molecular mechanics
• Electronic structure theory
• De novo methods
• Ab initio modeling
• Sequence-based modeling
• Threading
• Structural Plant Biology

This is a cost-effective approach for determining the protein structure. The   computational prediction methods, such as initiating fragment assembly, advanced fold recognition, composite approaches, and molecular docking are regularly applied in recent times to expand our understanding on protein structures. However, speculating the structures of proteins remains a confront, with congestions from both force field and conformational search.  Hybrid approach is a way to overcome these disadvantages, by including the limited experimental measurements, reliable structures that can be computed, and unlikely predictions are eliminated. The current researches are showing great interest in this method of approach.

• Structure Identification
• Hybrid of experimental methods
• Hybrid of computational methods
• Hybrid approaches in complementing high-resolution structural biology
• Determining protein complex structures
• Integration of atomic detail crystallography
• NMR structures

Structural biology targets aiming in comprehending the biomolecules at atomic level. Every aspect related in structural biology research seems to be complicated. The emerging research methods proved to be success in solving many complexities such as determination and functionality annotations  of the protein structures in drug designing and the drug target locations. Today’s science is successful in determining the protein structures which are solved on a large scale; but the gap between available sequence data and structure data is enormous. Bridging the gap is one of the main challenges for computing science.

• Nano-machinery
• Network signaling
• Protein folding

The focus of a structural biologist is protein structure determination and drug design. Protein plays an important role in human body. Living things would not exist without proteins. The proteins are usually involved in all forms of expressions of the living organism. Most of the proteins are evolved in providing structure to the cell while the others tend to bin and carry vital molecules all through the body. Some proteins are involved in biochemical reactions in the body which are termed as enzymes. Others are involved in muscle contractions and immunity. Structure determination of proteins has always been a challenging filed. The complex areas in the field include viruses, pathogens, membrane proteins and signaling pathways. Novel progressions are being done in the arenas of nanopatterning and multi-scale modelling of cell signaling proteins.

• Membrane proteins
• Pathogens and viruses
• Nano patterning
• Multi-scale modeling for signaling proteins
• Macromolecular designing

Viruses show different morphologies in their shapes and sizes. These are smaller in structures than the bacteria. Though these are simpler as an individual, when formed in group they are exceptionally diverse both in replication strategies and structures. Many viruses are important human pathogens. Many techniques such as x-ray crystallography, NMR and cryo-EM are used to determine viral structures. These structure in-turn are used to develop anti-viral drugs and vaccines.

• X-ray crystallography
• Solution NMR spectroscopy
• Cryo-electron tomography

Molecular modelling exhibits all the hypothetical methods and computational procedures used to mimic the behavior of macromolecules. In conventional monoscale modeling and simulation approaches, the scope and validity of a biological model is restricted to a specific time and space scale.

Molecular simulation requires the use of the efficient computers in stimulating the interactions among the atoms to study the material properties, these simulations based on the methods help in the quantum mechanical results ranging from atoms to clusters of molecules based on the time from milliseconds or longer.  Molecular Graphics helps in characterizing the global and local properties of molecules, processes and chemical reactions.

The techniques are applied in various emerging fields like drug designing in labs, computational chemistry, materials science and computational biology for studying macromolecular systems ranging from small to large biological systems. The techniques are performed using the computers for modelling, research studies, properties of atoms and molecular interactions.  

• Drug design
• Materials Science
• Protein folding
• Enzyme catalysis
• Protein stability
• Conformational changes associated with biomolecular function
• Molecular recognition of proteins, DNA and membrane complexes

Sequence analysis can be explained as a process of exposing DNA, RNA or peptide sequence to a wide range of analytical methods in order to understand its structure, function and evolution. The methods include sequence alignment, biological databases. The sequences are being compared to that of the known functions, harmoniously to understand the biology of the organism which gives the new sequence. Synergistic use of three-dimensional structures and deep sequencing is done to realize the effect of personalized medicine.

• Profile comparison
• Sequence assembly
• Gene prediction
• Protein Structure Prediction
• Membrane protein structure and function using complementary methods
• Deep sequencing for protein structure determination
• Synergistic use of 3D structures and deep sequencing to realize personalized medicine
• Deep sequencing for cancer studies
• Deep sequencing of HIV

A database is an organized collection of data. As a result of enormous research which is being done in Structural biology massive data has been produced. In order to assemble the data in a catalogued manner, bioinformatics databases are used. Various databases have been created to store biological data, such as sequence databases, structure databases, signaling pathway databases, etc.

• Protein data bank
• Electron microscopy data bank
• Protein structure classification database
• Classification of structural database
• Classification of protein structure

Generally, cells communicate by the release of chemical signals. They are often secreted from the cell and released into the extracellular space. Regulation of gene expression comprises a comprehensive range of mechanisms that are used by cells to regulate the production of specific gene products, and is familiarly termed as gene regulation. Sophisticated programs of gene expression are extensively observed in biology, for example to trigger developmental pathways, adapt to new food sources, or respond to environmental stimuli. Eventually the gene expressions can be adjusted, starting from transcription, initiation to post translation modification of a protein.

• Protein crystallography
• Adrenergic receptor
• G-protein-coupled receptor
• GPCR
• Protein structure

Bionanotechnology is a rapidly advancing area of scientific and technical opportunity that applies the tool and process of nano-fabrication to build designs to understand biosystem. Bionanotechnology is the adaptation of natural biosystems to develop similar nanomaterials. It offers at the nanoscale (100,000 times smaller than the diameter of the average human hair) the ability to provide insight into the structural features of biological systems such as cell or tissue as well as to develop nano-biomaterials & medical units for diagnostics, therapeutics and tissue regeneration.

• Antibody-Conjugated Nanoparticles
• Nanopore sequencing 
• Tissue engineering
• Nanoprobes
• Drug designs
• Detection techniques
• CNTs baised therapeutics

Genome Informatics plays a major role in computational biology in the development of tools for DNA sequence information and analysis, gene mapping, genetic variation, complex trait mapping, predict protein sequence and structure. Next Generation sequencing results in large amounts of long or short DNA reads requiring assembly process to generate the complete genome sequence. De novo genome assembler programs have been written to detect overlaps between reads, to assemble overlaps into contigs, and then combine contigs into scaffolds obtaining a draft genome sequence.

There is scope in the development and maintenance of databases of genomic and genetic data which include new tools for annotating complex genomes to expand their utility.

• Sequencing
• Assembly
• Annotation

Analysis and prediction of 3D-structures of macromolecules such as proteins, RNA, and DNA by computational methods has brought biological insights and global prospective. Structural bioinformatics tools have been developed, evaluated, applied to answer specific questions concerning a broad range of topics. Structural bioinformatics databases offer enormous possibilities for gathering analysis of available information about biomacromolecules and in broadening the possibility of analysis.

• Protein Data Banks & Structural Classification
• Molecular Modelling
• Protein Structure Predictions

Structural biology is one of the emerging fields in science. Day to day many developments and advancements are taking place. Huge numbers of solved structures have exaggerated rapidly. The field of drug design and drug discovery has been advanced. Functional annotations are another field where progressions are rapidly evolving. Alterations in order to improve the effectiveness of prevailing tools can also be noted. Remarkable advances have been made in the areas of technical imaging and advancement of hybrid methods to understand the structure and function of proteins.

• Structure determination
• Technological Advances in Existing Methods
• New and Potentially Disruptive Technologies
• Advances in Drug Design
• Advances in Tool Development
• Advances in imaging Technologies