Databases alignments

Tools of Bioinformatics Databases, Alignments, Structural Mapping... 

Database clustered fragments to reduce library size [134] fit by comparison of internal distance Cm matrices Database Alignment of multiple structures related to target to define variable regions (VR s) database fragments aligned to Ca steric check, build side chains with overlap, restrained minimization... 

Hidden Markov model (HMM) generation from a set of related sequences and use of this model to search databases, align sequences, and generate new sequences (HMMER suite)... 

Barton G J1996. Protein Sequence Alignment and Database Scanning. In Sternberg M E (Editor) Prote Structure Prediction - A Practical Approach. Oxford, IRL Press, pp. 31-63. 

Holm L and C Sander 1994. The FSSP Database of Structurally Aligned Protein Fold Families. Ni Acids Research 22 3600-3609. 

The functionality available in MedChem Explorer is broken down into a list of available computational experiments, including activity prediction, align/ pharmacophore, overlay molecules, conformer generation, property calculation, and database access. Within each experiment, the Web system walks the user through a series of questions that must be answered sequentially. The task is then submitted to a remote server, where it is performed. The user can view the progress of the work in their Web browser at any time. Once complete, the results of the calculation are stored on the server. The user can then run subsequent experiments starting with those results. The Web interface includes links to help pages at every step of the process. 

The molecular overlay experiment orients the molecules to hnd the best RMS or held ht. The held ht is based on electrostatic and steric interactions. The application can hnd either the best total alignment of all molecules or the best match of all molecules to a specihed target molecule. Alignment can include a database search for conformers that show the best alignment based on the molecules under study. 

Figure 12 ModBase, a database of comparative protein stracture models. Screenshots of the following ModBase panels are shown A form for searching for the models of a given protein, summary of the search results, summary of the models of a given protein, details about a single model, alignment on which a given model was based, 3D model displayed by RASMOL [237], and a model evaluation by the Prosall profile [217],...

GJ Barton. Protein sequence alignment and database scanning. In MJE Sternberg, ed. Protein Structure Prediction A Practical Approach. Oxford, UK IRE Press at Oxford Univ Press, 1998. 

GD Schuler. Sequence alignment and database searching. Methods Biochem Anal 39 145-171, 1998. 

A Sail, JP Overmgton. Derivation of rules for comparative protein modeling from a database of protein stiaicture alignments. Protein Sci 3 1582-1596, 1994. 

C Sander, R Schneider. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9 56-68, 1991. 

C Dodge, R Schneider, C Sander. The HSSP database of protein stiaicture-sequence alignments and family profiles. Nucleic Acids Res 26 313-315, 1998. 

S Henikoff, JG Henikoff, S Pietrokovski. BLOCKS+ A non-redundant database of protein alignment blocks derived from multiple compilations. Biomformatics 15 471-479, 1999. 

Sonnhammer, E.L., Eddy, S.R., Durbin, R. Pfam a comprehensive database of protein domain families based on seed alignments. Proteins 28 405-420, 1997. 

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