Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

BLAST program is widely used tool to find protein and DNA databases for sequence similarities. For protein comparisons, various definitions, algorithmic and statistical improvements described here allows the BLAST program execution time will decrease substantially while increasing their sensitivity to weak similarity.

New criteria to trigger the expansion of word hits, combined with new heuristics to generate gapped alignments, resulting in a gapped BLAST program that runs about three times the original speed.

Moreover, the method was introduced to automatically incorporate statistically significant alignments generated by BLAST into position-specific score matrix, and search the database using this matrix.

The resulting Position-Specific Iterated BLAST (PSI-BLAST) program running at approximately the same rate per iteration as gapped BLAST, but in many cases much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to some new and interesting members of BRCT reveal superfamily.

Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications.

A method has been designed for electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets. The method produces quantitative transfer of ribosomal protein gel containing urea. For sodium dodecyl sulfate gels, the original band pattern is obtained without loss of resolution, but the transfer is not quantitative.

This method allows the detection of proteins by autoradiography and simpler than conventional procedures. The immobilized proteins were detected by immunological procedures.

All additional binding capacity on the nitrocellulose was blocked with excess protein; then the specific antibody bound and, finally, a second antibody directed against the first antibody. The second antibody either radioactively labeled or fluorescein or peroxidase conjugate.

Certain proteins are then detected by either autoradiography, under UV light, or with a peroxidase reaction product, respectively. In the latter case, as little as 100 pg of protein clearly detectable. It is anticipated that the procedure will be applicable to the analysis of various proteins with a particular reaction or a ligand.

High-resolution two-dimensional electrophoresis of proteins.

A technique has been developed for the separation of proteins by two-dimensional polyacrylamide gel electrophoresis. Because the resolution and sensitivity, this technique is a powerful tool for the analysis and detection of proteins from biological sources are complex.

Proteins are separated according to the isoelectric point by isoelectric focusing in the first dimension, and according to molecular weight by sodium dodecyl sulfate electrophoresis in the second dimension. Since these two parameters are not related, it is possible to obtain nearly uniform distribution of protein spots on the gel-diminsional.

This technique has been completed in 1100 the different components of Escherichia coli and should be able to complete a maximum of 5000 proteins. A protein that contains as little as one disintegration per minute either 14C or 35S can be detected by autoradiography. A protein which is 10 minus 4 to 10 minus 5% of the total protein can be detected and quantified by autoradiography.

Reproducibility enough separation to allow any place in one of the separation to be matched to a different place in the separation. This technique provides a method to estimate (on the sensitivity described) of the amount of protein made by biological systems.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

This system can cope with different proteins in a single charge and can consequently be used in the analysis of in vivo modification results in changes in the cost.

Proteins are responsible for altered by missense mutations can be identified. A detailed description of the methods and characteristics of this system is presented.

Comparative protein modeling by satisfaction of spatial restrictions.

We describe a comparative protein modeling methods designed to find the most likely structure for a particular sequence alignment with related structures.

Three-dimensional (3D) model is obtained with a satisfactory optimal spatial limitation comes from the harmony and expressed as a probability density function (PDF) for a feature retained. For example, the probability for the main-chain conformation residues models can be controlled by the type residue, main-chain conformation of similar residues in proteins related, and local similarity between two sequences.

Some PDF is obtained from the correlation between structural features in 17 families of homologous proteins that are aligned on the basis of their 3D structure. The PDF withstand C-C distance alpha alpha, main-chain N-O distance, the main-chain and side chain dihedral angles.

A smoothing procedure is used in the derivation of this relationship is to minimize problems rarely database. 3D models of protein molecules obtained by optimizing pdf restrictions that violate the model inputs as little as possible.

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Pdf molecules derived as a combination of PDF withstand individual spatial features of the whole molecule. The optimization procedure is a method that applies a variable target function conjugate gradient algorithm for the position of all non-hydrogen atoms. This method is automated and illustrated by trypsin modeling of two other serine proteinase.

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