Frontiers in Genetics, 2022 Lysine glutarylation is a post-translational modification (PTM) that plays a regulatory role in various physiological and biological processes. Identifying glutarylated peptides using proteomic techniques is expensive and time-consuming.
Fatma Indriani +4 more
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Statistical Models of the Protein Fitness Landscape: Applications to Protein Evolution and Engineering [PDF]
, 2012 Understanding the protein fitness landscape is important for describing how natural proteins evolve and for engineering new proteins with useful properties.
Romero, Philip Anthony
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Exploiting Sparse Statistics for a Sequence-Based Prediction of the Effect of Mutations
Algorithms, 2019 Recent work showed that there is a significant difference between the statistics of amino acid triplets and quadruplets in sequences of folded proteins and randomly generated sequences.
Mihaly Mezei
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Predicting the Disease Risk of Protein Mutation Sequences With Pre-training Model
Frontiers in Genetics, 2020 Accurately identifying the missense mutations is of great help to alleviate the loss of protein function and structural changes, which might greatly reduce the risk of disease for tumor suppressor genes (e.g., BRCA1 and PTEN). In this paper, we propose a
Kuan Li +4 more
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Sequence-to-Structure Relation in Proteins-Amyloidogenic Proteins with Chameleon Sequences [PDF]
Journal of Proteomics & Bioinformatics, 2016 The existence of polypeptide chain fragments in which identical sequences translate into different secondary folds gives rise to questions concerning the structural variability associated with amyloidogenesis. In this paper the structural contribution of identical sequences to a common hydrophobic core is assessed on the basis of the fuzzy oil
Banach, Mateusz +3 more
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Rose: Generating Sequence Families [PDF]
, 1997 Stoye J, Evers D, Meyer F. Rose: Generating Sequence Families. Forschungsberichte.
Stoye, Jens ; https://orcid.org/ +2 more
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Computational Protein Design Force Field Optimization: A Negative Design Approach [PDF]
, 2007 An accurate force field is essential to computational protein design and protein folding studies. Proper force field tuning is problematic, however, due in part to the incomplete modeling of the unfolded state.
Alvizo, Oscar
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Methods for comparing a DNA sequence with a protein sequence [PDF]
Bioinformatics, 1996 We describe two methods for constructing an optimal global alignment of, and an optimal local alignment between, a DNA sequence and a protein sequence. The alignment model of the methods addresses the problems of frameshifts and introns in the DNA sequence. The methods require computer memory proportional to the sequence lengths, so they can rigorously
Huang, Xiaoqiu, Zhang, Jinghui
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The CATH database: an extended protein family resource for structural and functional genomics [PDF]
, 2003 The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath_new) currently contains 34 287 domain structures classified into 1383 superfamilies and 3285 sequence families.
Pearl, F.M.G. +8 more
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Multi-class protein fold classification using a new ensemble machine learning approach. [PDF]
, 2003 Protein structure classification represents an important process in understanding the associations between sequence and structure as well as possible functional and evolutionary relationships.
Deville, Y, Gilbert, D, Tan, A
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