Proteins 3D structures

U Lessel, D Schomburg. Similarities between protein 3D structures. Protein Eng 7 1175-1187, 1994. 

Provides coordinates for protein 3D structure and manipulation Provides coordinates for protein 3D structure and manipulation Sequence retrieval system for cross-referencing databases... 

BLAST Chime Entrez (NCBI) FASTA GenBank (NCBI) Molecules R Us RasMol (Ras Mac) SRS (EMBL) Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences Provides coordinates for protein 3D structure and manipulation Provides coordinates for protein 3D structure and manipulation Sequence retrieval system for cross referencing databases... 

Considering the availability of the 20 proteinogenic amino acids, a protein of an average size of about 250 amino acids can form 20250 possibilities of linear combinations, and thus cover 20250 or 4 x 10287 points in sequence space. Even if only a very small fraction, such as 1 in 1010 can form a three-dimensional structure, there would exist more protein 3D structures than atoms in the universe. As this clearly is not the case, given the just over 10 000 protein structures (Chapter 14, Section 14.3), nature so far could only probe a small fraction of the possible structures, which opens up opportunities to achieve success in improving enzymes in the test tube. The starting point is an enzyme with a measurable desired activity which still has to be improved. 

The current situation in bioinformatics is characterized by an avalanche of DNA sequences from the human genome project and similar programs and, consequently, an exponential increase in DNA sequences but only a linear increase in protein 3D structures. While multitudes of putative genes have been annotated, up to 90% of all known DNA sequences have no assigned, i.e., experimentally proven, function. From this situation arise the need for interpretation of DNA sequences by information technology, and moreover, analysis of functional genomics and proteomics (see Chapter 15). 

Number of accessible protein 3D structures (PDB current holdings) ... 

Figure 16.1 Repeatedly used structural motifs of protein 3D structures (Branden, 1999) ...

Figure 4.11. Graphic representations of protein 3D structure. Three-dimensional graphics of hen s egg-white lysozyme as visualized with RasMol (first and second rows, ILYZ.pdb) and Cn3D (third row, ILYZ.val) are shown from left to right (color type) in wireframe (atom), spacefill (atom), dots (residue), backbone (residue), ribbons (secondary structure), strands (secondary structure), secondary structure (secondary structure), ball-and-stick (residue), and tubular (domain) representations.

Having such an efficient tool for predicting proteins 3D structure as the REFINER model, could we design a protein exhibiting the conformational autocatalysis ... 

Anderson PH, Nielsen M, Lund O (2006) Prediction of residues in discontinuous B-cell epitopes using protein 3D structure. Protein Sci 15 2558-2567... 

The GRID interaction energy values are stored in a matrix with a row for each protein 3D structure and m x k columns, corresponding to m probes x k GRID points. The structure of this matrix enables to consider multiple protein structures (reeNote 2). 

Domain assignment domains are basic building blocks of protein 3D structures. Several algorithms have been proposed to identify domains in a protein structure using criteria such as physico-chemical properties of amino acids in certain regions, e.g. hydrophobicity and accessibility, compactness of protein parts and their recurrence in other proteins [116-120]. 

Hoffmann, D. S., V. Wefing, Stephan, Albrecht, M., Hanisch, D., Zimmer, R., A new method for the fast solution of Protein-3D-Structures, combining experiments and bioinformatics. in Caesarium 2000. 2001. Bonn Springer Verlag. 

Kawabata, T. 2003. MATRAS A program for protein 3D structure comparison. Nucleic Acids Res 31 3367-9. 

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