Structure Prediction And Molecular Docking 1521 Ab initio Prediction of Protein Structure

It is well established that the sequence of the amino acid constituting a protein is of prime importance in the determination of its 3D structure and functional properties. Because sequence assignment is much faster and easier than 3D structure determination, the prediction of the 3D structure from the sequence of amino acids has been a great challenge for protein modeling (Bonneau and Baker, 2001). Energy-based structure prediction relies on energy minimization and molecular dynamics. The...

Dynamic Biochemistry Metabolic Simulation

Almost the same biochemical reactions occur in all living organisms. These reactions, known as primary metabolism, are organized into catabolic pathways and anabolic pathways. In addition, specialized biochemical transformations, known as secondary metabolism, are found in specialized tissues of some organisms. Xenometabolism refers to biochemical reactions that transform foreign compounds. Internet resources for retrieving metabolic information are presented. Biochemical reactions are subject...

Toward 3D Structure Prediction Structural Similarity Classification and Folds

The structural similarity search can be conducted at Jpred if the Bypass on the current Brookhaven Protein Database box is unchecked. The search returns output for the pairwise alignments of the query sequence against the sequences of PDB files with the consensus sequence between them and the summary of the alignments. The G To P site http spock.genes.nig.ac.jp genome gtop.html provides BLAST and PSI-BLAST searches of a query sequence against 3D structures PDB or SCOP . Select either BLAST...

Approaches To Gene Identification

Genomics conducts structural and functional studies of genomes McKusick, 1997 Shapiro and Harris, 2000 Starkey and Elaswarapu, 2001 . The former deals with the determination of DNA sequences and gene mapping, while the latter is concerned with the attachment of functional information to existing structural knowledge about DNA sequences. Genome database mining refers to the process of computational genome annotation by which uncharacterized DNA sequence is documented by the location along the...

Display of 3D Structures with Molecular Graphics Programs

Alcohol Dehydrogenase Viewerlite

For the 3D view of ISIS Draw, ACD 3D Viewer Add-in can be installed. Retrieve ACD 3D Viewer for ISIS Draw from http www.acdlabs.com downloar download.cgi and installed it as an Add-in according to instructions. To view 3D structure which is opened sketched on the ISIS Draw window, select ACD 3D Viewer tool from Object menu to open ACD 3D Viewer window and subsequent display of the 3D structure. The 3D structure can be optimized and can be saved only in .s3d format, which is not recognizable by...

Drawing of Molecular Structures

The 1D nucleotide amino acid sequences in character format without index, e.g., fasta format can be converted into the 2D chemical structures with ISIS Draw, which can be downloaded from MDL Information System at http www.mdli.com download isisdraw.html for academic use. Install the package by issuing Run command, C Isis Draw23.exe. Launch IsisDraw to open the Draw window. Retrieve nucleotide amino acid sequence file in fasta format remove the heading, gt line or prepare text file of sequence...

Proteomics Protein Sequence Analysis

Proteomics is concerned with the analysis of the complete protein complements of genomes. Thus proteomics includes not only the identification and quantification of proteins, but also the determination of their localization, modifications, interactions, activities, and functions. This chapter focuses on protein sequences as the sources of biochemical information. Protein sequence databases are surveyed. Similarity search and sequence alignments using the Internet resources are described. 11.1....

Biopolymer Modeling at B Biopolymer Server

The B server http www.scripps.edu nwhite B indexFrames.htmp offers an online biomolecular modeling program that builds biomolecular models, measures their geometry, and implements an AMBER force field in the geometry optimization as well as in molecular dynamics. The Biomer authentication certificate see http www.scripps.edu nwhite B Security is required to enable opening saving files though it is not needed to run the B program . Click the Start B button to open the B window. Hit the Grant...

Energy Minimization and Geometry Optimization

The basic task in the computational portion of MM is to minimize the strain energy of the molecule by altering the atomic positions to optimal geometry. This means minimizing the total nonlinear strain energy represented by the FF equation with respect to the independent variables, which are the Cartesian coordinates of the atoms Altona and Faber, 1974 . The following issues are related to the energy minimization of a molecular structure The most stable configuration of a molecule can be found...

Analysis of Binding Data

DynaFit Kuzmic, 1996 , which can be downloaded for academic use from http www.biokin.com , is a versatile program for statistical analysis and fitting of the equilibrium binding data, the initial velocities, and the time course of enzymatic reactions according to the user defined mechanisms. The program performs nonlinear least-squares regression of ligand-receptor binding and enzyme kinetic data. To run DynaFit, you must first create a user subdirectory into which you should place a script...

Application of Hyper Chem

HyperChem is the PC-based molecular modeling and simulation software package marketed by Hypercube Inc. http www.hyper.com . The program provides molecular mechanics with MM , AMBER, BIO CHARMm , and OPLS force fields , semiempirical extented Hlickel, CNDO, INDO, MINDO3, MNDO, AM1, PM3, and ZINDO , and ab initio quantum mechanics calculations. Computations are carried out for single-point energy, geometry optimization energy minimization , molecular dynamics, Langevin dynamics, Monte Carlo...