Journal ArticleDOI
Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures.
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TLDR
It is shown that a pattern of hydrophobicity values derived from a set of related protein sequences is well correlated with the linear pattern of side‐chain solvent accessibility values, calculated from a known protein structure representative of the sequences.Abstract:
Hydrophobic side chains often are buried in the interior of a protein, and evolutionarily related proteins usually maintain the hydrophobic character of buried positions. In this paper we show that a pattern of hydrophobicity values derived from a set of related protein sequences is well correlated with the linear pattern of side-chain solvent accessibility values, calculated from a known protein structure representative of the sequences. In several cases, information from aligned sequences can be used to select the correct tertiary fold from a large data base of protein structures.read more
Citations
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Journal ArticleDOI
Deciphering the message in protein sequences: tolerance to amino acid substitutions
TL;DR: Comparison of different sequences with similar messages can reveal key features of the code and improve understanding of how a protein folds and how it performs its function.
Journal ArticleDOI
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
TL;DR: The effects of multiple sequence information and different types of conformational constraints on the overall performance of the method are investigated, and the ability of a variety of recently developed scoring functions to recognize the native-like conformations in the ensembles of simulated structures are investigated.
Journal ArticleDOI
Protein design by binary patterning of polar and nonpolar amino acids
Satwik Kamtekar,Jarad M. Schiffer,Jarad M. Schiffer,Huayu Xiong,Jennifer M. Babik,Michael H. Hecht +5 more
TL;DR: A simple binary code of polar and nonpolar residues arranged in the appropriate order can drive polypeptide chains to collapse into globular alpha-helical folds.
Journal ArticleDOI
An empirical energy function for threading protein sequence through the folding motif
TL;DR: It is suggested that contact potentials reflect important constraints on nonbonded interaction in native proteins, and that “threading” may be useful for structure prediction by recognition of folding motif.
Journal ArticleDOI
Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures.
TL;DR: The basic physical principles of Boltzmann's principle for protein folding are outlined and several techniques which are useful in the development of knowledge-based force fields are summarized.
References
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Journal ArticleDOI
A comprehensive set of sequence analysis programs for the VAX
TL;DR: A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system.
Journal ArticleDOI
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
TL;DR: A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
Journal ArticleDOI
A general method applicable to the search for similarities in the amino acid sequence of two proteins
TL;DR: A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed and it is possible to determine whether significant homology exists between the proteins to trace their possible evolutionary development.
Journal ArticleDOI
The Protein Data Bank: a computer-based archival file for macromolecular structures.
Frances C. Bernstein,Thomas F. Koetzle,Graheme J. B. Williams,Edgar F. Meyer,Michael D. Brice,John R. Rodgers,O. Kennard,Takehiko Shimanouchi,Mitsuo Tasumi +8 more
TL;DR: The Protein Data Bank is a computer-based archival file for macromolecular structures that stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies.
Journal ArticleDOI
The interpretation of protein structures: estimation of static accessibility.
B. Lee,Frederic M. Richards +1 more
TL;DR: The accessibility of atoms in the twenty common amino acids in model tripeptides of the type Ala-X-Ala are given for defined conformation and the larger non-polar amino acids tend to be more “buried” in the native form of all three proteins.