Homologous protein structures

CA Schiffer, JW Caldwell, PA Kollman, RM Stroud. Prediction of homologous protein structures based on conformational searches and energetics. Pi otems 8 30-43, 1990. 

Protein-based methods rely upon the structural information extracted from the X-ray crystallographic and/or homology protein structures. These also include docking techniques for the exploration of possible binding modes of a ligand to a given transporter protein. 

Balaji S, Sujatha S, Knmarm SS et al (2001) PALI-a database of Phylogeny and ALIgnment of homologous protein structures. Nucleic Acids Res 29 61-65... 

Mention has already been made of homologous protein structures. They represent examples of extensive similarities which are so conspicious and generally known that they do not require any further discussion, even though they are direct proofs of specific amino acid replacements. The fact that the same types of regularities as those which have already been... 

Abbreviations used in table (see also caption to Table 5.2) HB -hydrogen bonding potential energy term self-bb - prediction of side-chain conformation on to template backbone of modeled sequence non-self - prediction of side-chain conformation onto backbone borrowed from a homologous protein structure. 

Xiang, Z. (2006) Advances in homology protein structure modeling. Current Protein Peptide Science, 7 (3), 217-227. 

Recent Developments of the Homologous Protein Structure Alignment Database. 

MJ Sutcliffe, I Haneef, D Carney, TL Blundell. Knowledge based modelling of homologous proteins. Part I Three dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng 1 377-384, 1987. 

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

P Koehl, M Delame. A self consistent mean field approach to simultaneous gap closure and side-chain positioning m protein homology modelling. Nature Struct Biol 2 163-170, 1995. R Samudrala, J Moult. A graph-theoretic algorithm for comparative modeling of protein structure. J Mol Biol 279 287-302, 1998. 

MAS Saqi, PA Bates, MJE Sternberg. Towards an automatic method of predicting protein structure by homology An evaluation of suboptimal sequence alignments. Protein Eng 5 305-311, 1992. 

An effective method for localizing causes of redox potentials is to plot the total backbone and side chain contributions to ( ) per residue for homologous proteins as functions of the residue number using a consensus sequence, with insertions treated by summing the contribution of the entire insertion as one residue. The results for homologous proteins should be examined for differences in the contributions to ( ) per residue that correlate with observed redox potential differences. These differences can then be correlated with any other sequence-redox potential data for proteins that lack crystal or NMR structures. In addition, any sequences of homologous proteins that lack both redox potentials and structures should be examined, because residues important in defining the redox potential are likely to have semi-sequence conservation of a few key amino acid types. 

Homologous proteins have similar structure and function... 

Homologous proteins have conserved structural cores and variable loop regions... 

Prediction methods for secondary structure benefit from multiple alignment of homologous proteins... 

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