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

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Topology fingerprint approach to the inverse protein folding problem

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

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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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Self-citation

Authors: Godzik, A., Kolinski, A., & Skolnick, J.
Affiliations: Scripps Research Institute (US)
Corresponding author: Skolnick, Jeffrey
ORCID: Godzik, Adam
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)
DOI: 10.1016/0022-2836(92)90693-e
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
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
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
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › 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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Topology fingerprint approach to the inverse protein folding problem

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