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Literature DB >> 11893514

Getting the most from PSI-BLAST.

Abstract

Most biologists now conduct sequence searches as a matter of course. But how do we know that a relationship predicted by a homology search is a true, rather than false, hit with the same score? Many biologists design their own experiments with exquisite care yet still assume that results from programs with more than 20 adjustable parameters are 100% reliable. This article explains some of the key steps in getting the most from PSI-Blast, one of the most popular and powerful homology search programs currently available.

Mesh：

Substances：
Proteins
DNA

Year: 2002 PMID： 11893514 DOI： 10.1016/s0968-0004(01)02039-4

Source DB: PubMed Journal: Trends Biochem Sci ISSN： 0968-0004 Impact factor: 13.807

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Cited

48 in total

1. The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds.

Authors: Parag Mallick; Robert Weiss; David Eisenberg
Journal: Proc Natl Acad Sci U S A Date: 2002-12-02 Impact factor: 11.205

2. Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.

Authors: Alexander Stark; Robert B Russell
Journal: Nucleic Acids Res Date: 2003-07-01 Impact factor: 16.971

3. MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins.

Authors: Fatemeh Miri Disfani; Wei-Lun Hsu; Marcin J Mizianty; Christopher J Oldfield; Bin Xue; A Keith Dunker; Vladimir N Uversky; Lukasz Kurgan
Journal: Bioinformatics Date: 2012-06-15 Impact factor: 6.937

Review 4. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

Authors: Khader Shameer; Lokesh P Tripathi; Krishna R Kalari; Joel T Dudley; Ramanathan Sowdhamini
Journal: Brief Bioinform Date: 2015-10-22 Impact factor: 11.622

Getting the most from PSI-BLAST.

1. The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds.

2. Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.

3. MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins.

Review 4. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

5. Assessing strategies for improved superfamily recognition.

6. Effective function annotation through catalytic residue conservation.

7. Functional annotation prediction: all for one and one for all.

8. Prediction of protein function improving sequence remote alignment search by a fuzzy logic algorithm.

Review 9. Novel bacterial ADP-ribosylating toxins: structure and function.

10. Protein subcellular localization prediction of eukaryotes using a knowledge-based approach.