Computation in BioInformatics. Группа авторов
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Название: Computation in BioInformatics

Автор: Группа авторов

Издательство: John Wiley & Sons Limited

Жанр: Базы данных

Серия:

isbn: 9781119654766

isbn:

СКАЧАТЬ Computed Atlas of Surface Topography of proteins (CASTp) is an online resource which is used for locating, delineating and measuring of concave surface regions on the 3D structures of protein [13]. It includes pockets which are located on protein surfaces. This server can be used to study surface features and functional regions of proteins. The server is updated daily and can be accessed at http://cast.engr.uic.edu

       Active Site Prediction Server: Active Site Prediction of Protein server help in computing the cavities in a given target protein. This sever can be easily accessed at http://www.scfbio-iitd.res.in/dock/ActiveSite_new.jsp.

       3DLigandSite: It is an automated method which can predict the ligand binding sites. One can submit a sequence or a protein structure and once submitted Phyre is run to predict the structure. The structure can then be used to search a structural library in order to identify homologous structures with bound ligands. These ligands are then superimposed onto the protein structure in order to predict a ligand binding site [14]. It can be accessed at http://www.sbg.bio.ic.ac.uk/3dligandsite.

      1.2.3 Molecular Modeling

      1 a) Recognition of template and sequence alignment: Recognition of the template is the beginning step in homology modeling. To identify the homologous sequences of unknown protein, one can search the unknown against the pre-existing ones whose structure is known and identified. The homologous sequences can be identified by similarity searches which can be performed using sequence alignment programs such as BLAST (Basic Local Alignment Search Tool).

      2 b) Model building: Some of the methods involved in building a model are spatial restraint, rigid-body assembly, segment matching, and artificial evolution.

      3 c) Refinement modeling: Refinement of model involves addition, deletion, and substitution of amino acid residues, which includes loop modeling and side-chain modeling. This kind of modeling is based on molecular dynamics simulations, genetic algorithms, and Monte Carlo methods. AMBER, CHARMM22, and MM3 are commonly used force fields for energy minimization of modeled structures.1. Loop modeling: In homologous protein sequences, insertion and substitution of amino acid residues in variable portion of the protein are referred as loops.2. Side-chain modeling: It involves substitution of the side chains on the backbone structure of the protein. The substitution is analyzed by Root Mean Square Deviation (RMSD) values.

      4 d) Validation of modeled protein structure: The protein structure obtained after homology modeling needs to be validated in order to check the accuracy of the modeling. This can be performed using web servers like WHATCHECK, WHAT IF, VADAR, and PROCHECK.

      5 e) Small molecule databases: Screening of compounds in drug discovery to identify novel and drug-like properties can be performed using small molecule databases like NCBI, PubChem, and ChEMBL [19].

S. no. Name of software Description Reference
1 MODELLER It involves homology modeling of the three-dimensional structures of the target protein. [20]
2 UCSF Chimera It helps in the visualization and analysis of molecular structures. [21]
3 SWISS PDB VIEWER It allows to analyze and model proteins. [22]
4 Geno3D It is an automatic web server for protein molecular modeling. [23]
5 SWISS MODEL Automated comparative modeling of protein structures can be performed. [24]
6 CCP4 It helps in macromolecular structure determination. [25]
7 Abalone It is a modeling program which involves molecular dynamics of biopolymers [26]
8 Tinker It performs molecular mechanics and dynamics along with some unique features for biopolymers. [27]

       MODELLER: It is a computer program which models 3D structures of proteins and their assemblies. This program is the most frequently used program for homology modeling. In order to construct, one needs to provide aligned sequence which will be modeled with known structures [27]. The program will then easily construct/build a model with no hydrogen atoms (https://salilab.org/modeller/).

       SWISS PDB VIEWER: The Swiss PDB Viewer is a free molecular graphics program that helps us to evaluate various proteins at the same time. The proteins can be placed one on top of another to reason the structural alignments and compare their active sites [28]. This program can be easily accessed at https://spdbv.vital-it.ch/.

       SWISS MODEL: It is СКАЧАТЬ