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May 3rd, 2024: Geno3D updated (see NEWS).
References
BLAST
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic Acids Res, 1997, 25:3389-3402.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a
variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be
decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word
hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three
times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments
produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific
Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more
sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of
the BRCT superfamily.
CNS
Crystallography & NMR : A new software suite for macromolecular structure determination.
Acta Cryst, 1998, 54, 905-921.
Brunger AT, Adams PD, Clore GM, Delano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu, NS, Read RJ, Rice LM, Simonson T, Warren GL.
A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing structure-determination programs, the architecture of CNS is highly flexible, allowing for extension to other structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic structure-determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data structures, such as structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of macromolecular structure determination by X-ray crystallography and solution NMR.
Geno3D
Geno3D: Automatic comparative molecular modelling of protein.
Bioinformatics, 2002, 18:213-214.
Combet C, Jambon M, Deléage G, Geourjon C.
Geno3D is an automatic web server for protein molecular modelling. Starting with a query protein sequence, the server performs the homology modelling in six successive steps: (i) identify homologous proteins with known 3D structures by using PSI-BLAST; (ii) provide the user all potential templates through a very convenient user interface for target selection; (iii) perform the alignment of both query and subject sequences; (iv) extract geometrical restraints (dihedral angles and distances) for corresponding atoms between the query and the template; (v) perform the 3D construction of the protein by using a distance geometry approach and (vi) finally send the results by e-mail to the user.
PROCHECK
PROCHECK: a program to check the stereochemical quality of protein structures.
J Appl Cryst, 1993, 26, 283–291.
Laskowski RA, MacArthur MW, Moss DS and Thornton JM.
The PROCHECK suite of programs provides a detailed check on the stereochemistry of a protein structure. Its outputs comprise a number of plots in PostScript format and a comprehensive residue-by-residue listing. These give an assessment of the overall quality of the structure as compared with well refined structures of the same resolution and also highlight regions that may need further investigation. The PROCHECK programs are useful for assessing the quality not only of protein structures in the process of being solved but also of existing structures and of those being modelled on known structures.
Sov parameter
Identification of related proteins with weak sequence identity using secondary structure information.
Protein Sci, 2001, 10:788-97.
Geourjon C, Combet C, Blanchet C, Deléage G.
Molecular modeling of proteins is confronted with the problem of finding homologous proteins, especially when few identities remain after the process of molecular evolution. Using even the most recent methods based on sequence identity detection, structural relationships are still difficult to establish with high reliability. As protein structures are more conserved than sequences, we investigated the possibility of using protein secondary structure comparison (observed or predicted structures) to discriminate between related and unrelated proteins sequences in the range of 10%-30% sequence identity. Pairwise comparison of secondary structures have been measured using the structural overlap (Sov) parameter. In this article, we show that if the secondary structures likeness is >50%, most of the pairs are structurally related. Taking into account the secondary structures of proteins that have been detected by BLAST, FASTA, or SSEARCH in the noisy region (with high E: value), we show that distantly related protein sequences (even with <20% identity) can be still identified. This strategy can be used to identify three-dimensional templates in homology modeling by finding unexpected related proteins and to select proteins for experimental investigation in a structural genomic approach, as well as for genome annotation.
XPLO2D
Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?
Structure, 2003, 11:1051-9.
Kleywegt GJ, Henrick K, Dodson EJ, van Aalten DM.
For the refinement of protein and nucleic acid structures, high-quality geometric restraint libraries are available. Unfortunately, for other compounds, such as physiological ligands, lead compounds, substrate analogs, etc., the situation is not as favorable. As a result, the structures of small molecules found in complexes with biomacromolecules are often less reliable than those of the surrounding amino or nucleic acids. Here, we briefly review the use of geometric restraints in structure refinement (be it against X-ray crystallographic or NMR-derived data) and simulation. In addition, we discuss methods to generate both restraint libraries and (idealized) coordinates for small molecules and provide some practical advice.
Last modification time : Fri Apr 14 16:46:15 2023. Current time : Tue May 7 04:59:52 2024. User : public@18.225.11.98.
