Cited by 339Protein Structure and DynamicsEnzyme Structure and FunctionMachine Learning in Bioinformatics

Topology fingerprint approach to the inverse protein folding problem

Godzik, Adam, Kolinski, Andrzej, Skolnick, Jeffrey·1992·Journal of Molecular Biology

Abstract

We describe the most general solution to date of the problem of matching globular protein sequences to the appropriate three-dimensional structures. The screening template, against which sequences are tested, is provided by a protein "structural fingerprint" library based on the contact map and the buried/exposed pattern of residues. Then, a lattice Monte Carlo algorithm validates or dismisses the stability of the proposed fold. Examples of known structural similarities between proteins having weakly or unrelated sequences such as the globins and phycocyanins, the eight-member alpha/beta fold of triose phosphate isomerase and even a close structural equivalence between azurin and immunoglobulins are found.

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Crossref · 10.1016/0022-2836(92)90693-e

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Authors
Godzik, A., Kolinski, A., & Skolnick, J.
Affiliations
Scripps Research Institute (US)
Corresponding author
Skolnick, Jeffrey
Venue
Journal of Molecular Biology
Publisher
Elsevier BV
Published
1992-09
Volume
227
Issue
1
Pages
227-238
ISSN
0022-2836 (ISSN-L)
OpenAlex
W2040594319
Cited by
339
References
34
Citations by year
2025: 3 · 2022: 2 · 2021: 1 · 2020: 3 · 2018: 3 · 2017: 2 · 2016: 5 · 2015: 3 · 2014: 6 · 2013: 4 · 2012: 2
FWCI
7.82
Type
journal article
Language
en
Open access
closed
Locations
  • Journal of Molecular Biology (publishedVersion)
  • PubMed (publishedVersion)
Funders
National Institute of General Medical Sciences (GM 37408, R01GM037408)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Keywords
inverse protein folding, protein structure prediction, structural fingerprints, contact maps, lattice Monte Carlo simulation, globin, phycocyanin, triosephosphate isomerase, azurin, immunoglobulins, structural equivalence
MeSH terms
Algorithms, Azurin, Bacterial Outer Membrane Proteins, Bacterial Proteins, Globins, Immunoglobulin lambda-Chains, Models, Molecular, Phycocyanin, Plant Proteins, Plastocyanin, Protein Conformation, Structure-Activity Relationship, Thermodynamics, Databases, Factual, Sequence Alignment

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