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protein crystals insight into the structure and dynamics at micro level resolution like electron crystallography. With the help of AFM detailed information of structure and dynamics of membrane protein could be assessed. Cryoelectron microscopy: Cryoelectron microscopy produces 3D structures of proteins at atomic resolution. The combined application of cryoelectron microscopy with other microscopic techniques established 3D structure of different membrane proteins and allowed the visualization of conformational changes during catalytic cycles. Computational Methods: Molecular Simulation Techniques Computational based methods present an improvement for perceptive protein flexibility and stability as well. However, Molecular Dynamics (MD) simulation models render interactions among atoms of polypeptide chain. The Folding and unfolding pathways of Proteins Formation of the final native structure Time dependence of pathways (folding and unfolding) The inter-residue interactions that underlie the processes Table 1: Advantage of Molecular Dynamics (MD). Below is the list of molecular simulation techniques (Table 02) that are employed to investigate the various aspects of protein dynamics especially folding and unfolding, in silico. S.# Tools Particulars 1 ModView For the illustrating multiple protein sequences and structural analysis 2 Perturbation Analyzer Tool study for the protein network interactions 3 Protein Analyst Distributed object environment for protein sequence and structure analysis 4 VISTRAJ Exploring protein conformational space 5 PROTMAP2D Visualization, comparison and analysis of 2D maps of protein structure 6 FlexServ Integrated tool for the analysis of protein flexibility 7 iFold Platform for interactive folding simulations of proteins 8 Bio3d An R package for the comparative analysis of protein structures 9 PConPy Python module for generating 2D protein maps 10 COREX/BEST server Regional stability and thermodynamic aspects 11 CAVER 3.0 For the study of transport pathways 12 ExPASy (Expert Protein Analysis System) Bioinformatics resource portal 13 UniProt Database of protein sequence and functional information 14 RasMol For molecular graphics visualization 15 BLAST For comparing primary biological sequence information 16 T-coffee Multiple sequence alignment software ModView Table 2: Molecular Simulation Techniques. For the visualization of multiple protein sequences and structure analysis, a program has been introduced called ModView (a web based application). It facilitates the users with data base query engine, multiple sequence alignment editors, and multiple structure viewers. Users can control hundreds of proteins interactively, to create fragments, active and binding sites as well as domains in protein families to show macromolecular complexes of virus or ribosome. ModView, has been incorporated as plug-in in Netscape (an internet browser), along with text and figures that could be used for teaching and presentations [39]. Perturbation analyzer Perturbation analyzer has been developed for using with Cytoscape (a program for visualizing molecular interaction networks and integrating these interactions with gene expression profiles). Basically it is an open source plug-in and could be used in manual approach for simulating user defined perturbations, and help for estimating the network robustness and identification of significant proteins that produce large effects in protein network interactions (PINs), when concentrations are perturbed. It has a great deal in exploring the design principles of protein networks and could be a valuable for identifying drug target [40]. Protein Analyst Protein Analyst is a tool for the analysis of protein sequences with prominence on the integration of sequence and structural information. Protein Analyst is considered to be a flexible integrated tool for delivering existing and newly developed protein bioinformatics algorithms to the desktop with emphasis on the integration of sequence and structural information [41]. VISTRAJ VISTRAJ allows 3D visualization, handling and editing of protein conformational space with the help of probabilistic maps of the space. These probabilistic maps known as trajectories distributions and serve as input to FOLDTRAJ, while FOLDTRAJ generates sample protein structures based on conformational space. Both could be used as tools for homology model formation and 3D structures are produced containing post translational modified amino acids. FOLDTRAJ helps in generating plausible probabilistic protein conformers [42]. PROTMAP 2D Protein structure comparison is an elementary issue in the field of structural biology and bioinformatics. 2D maps regarding distances between residues contain information to restore the 3D representation. The maps disclose patterns of interaction between secondary and super-secondary structures and are helpful in visual investigations. The overlapping of the maps of to structures gives a measurement of protein structure similarity. PROTMAP 2D helps in calculation of contact and distance maps, based on user defined parameters, quantitative measurement of pairs or series of contact maps and visualization of the results [43]. OMICS Group eBooks 015
FlexServ The flexibility of proteins can be analyzed by FlexServ (a web-based program). The incorporated protocols in the server like normal mode analysis (NMA), discrete molecular dynamics (DMD) and Brownian dynamics are used for protein dynamics. User defined trajectories could also be analyzed. The server facilitates all the parameters related to the flexibility analysis e.g. temperature factors, basic geometrical analysis, inflexibility analysis, chain correlation, dynamic domain determination, essential dynamics etc. The complete data is illustrated by plain text, 2D and 3D graphics [44]. iFold Molecular simulations of protein dynamics could be performed by using iFold (web-based program). This server provides various features regarding protein folding of large scale simulations, thermodynamic analysis, pfold analysis and simulated annealing with the help of discrete molecular dynamics (DMD). Moreover, protein models could be generated by interactions among amino acids [45]. Bio3d The homologous structure of proteins is analyzed by using a computer program, Bio3d. It has great advantage of graphics as well as statistics. Homologous analysis helps in the study of internal conformational differences of structures and inter-conformer associations. Moreover, it facilitates the exploring of structural protein evolution. Various features of this program assist in exploring structure and sequences of proteins like dynamic trajectory data, sequence data, re-orientation, atom selection, sequence conservation analysis, distance matrix analysis, clustering analysis, principal component analysis (PCA) and rigid core analysis [46]. PConPy An open-source Python (A simple, high-level interpreted language) module for creating protein contact maps, distance maps and hydrogen bond plots. Contact maps can be explained with secondary structure and hydrogen bond assignments. These maps can be produced in a number of publication-quality vector and raster image formats. PConPy offers a more flexible choice of contact description parameters than existing toolkits. PConPy can be employed as stand-alone software or imported into existing source code (source language). A web-interface to PConPy is also available for use [47]. DYNATRAJ DYNATRAJ facilitates visualization of modes of motion and PCA for ensemble of protein structures taken from the molecular dynamics and experimental ensembles by using NMR. DYNAPOCKET: DYNA POCKET provides configuration of a protein pocket found in single protein structure. It helps in prediction of drug designing by using binding pocket conformations. COREX/BEST Server This server has ability to generate structural and thermodynamic aspects of protein structures. The conformational ensemble provides stability of protein structure and conformation. The stability of protein conformations are expressed by kcal/mol (units of energy). The stability of regions in the structure at the resolution of residues is mapped onto protein structure for visual expression [48]. CAVER CAVER is extensively employed for the study of transport pathways in protein macromolecular structures. The idea of tunnel and channels is crucial for the understanding of transport of small particles (polar or non-polar) through plasma membrane. The perceptiveness of association between structure and functionality of proteins helps in designing of new inhibitors and production of biocatalysts. CAVER 3.0 helps in the analysis of tunnel and channels in protein conformations. It also gives insight into clustering in pathways [49]. Figure 15: Caver 3.0 Paves the Technique for the Study of Essential Biochemical Mechanisms. ExPASy (Expert Protein Analysis System) ExPASy is a bioinformatics resource portal (gateway) operated by the Swiss Institute of Bioinformatics (SIB). It is an integrative portal accessing many databases, software tools and scientific resources in different areas of life sciences (proteomics, phylogeny/evolution, genomics, transcriptomics, systems biology, population genetics, etc). ExPASy acts as a proteomics server to analyze protein sequences and structures and two-dimensional (2D) gel electrophoresis [50]. UniProt UniProt is a freely accessible database of protein functional information and sequence as well as many entries being derived from genome sequencing projects. It consists of a large amount of information about the biological function of proteins derived from the OMICS Group eBooks 016
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purification methodology and laid t
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Affinity chromatography (AC): The p
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molecules such as proteins. Further
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New Peptide Based Therapeutic Appro
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ability to selectively target cells
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separation efficiency. However, use
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