4.8 Article

Discovering design principles of collagen molecular stability using a genetic algorithm, deep learning, and experimental validation

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Engineering, Biomedical

ColGen: An end-to-end deep learning model to predict thermal stability of de novo collagen sequences

Chi-Hua Yu et al.

Summary: Collagen is a crucial structural protein in human tissues, commonly used for repairs and regeneration, but designing specific collagen sequences remains a challenge. Research shows that mutations to glycines, mutations in the middle of a sequence, and short sequence lengths have the greatest impact on the stability of collagen structures.

JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS (2022)

Article Chemistry, Multidisciplinary

Predicting the stability of homotrimeric and heterotrimeric collagen helices

Douglas R. Walker et al.

Summary: The research developed an algorithm to predict the stability of collagen triple helices and guide the design of synthetic helices assembly. Through testing and optimization, the algorithm successfully guided the design of a heterotrimer possessing high assembly specificity.

NATURE CHEMISTRY (2021)

Article Chemistry, Medicinal

SMILES Pair Encoding: A Data-Driven Substructure Tokenization Algorithm for Deep Learning

Xinhao Li et al.

Summary: In this study, SMILES pair encoding (SPE) is introduced as a data-driven tokenization algorithm, which expands the atom-level tokenization by learning high-frequency SMILES substrings. The results demonstrate that SPE-based generative models outperform atom-level tokenization model in terms of novelty, diversity, and ability to resemble the training set distribution.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Review Computer Science, Information Systems

A review on genetic algorithm: past, present, and future

Sourabh Katoch et al.

Summary: This paper discusses recent advances in genetic algorithms, analyzing selected algorithms of interest in the research community. It helps new and demanding researchers gain a broader understanding of genetic algorithms. The review covers well-known algorithms, genetic operators, research domains, and future research directions in genetic algorithms.

MULTIMEDIA TOOLS AND APPLICATIONS (2021)

Article Materials Science, Biomaterials

Wave Propagation and Energy Dissipation in Collagen Molecules

Mario Milazzo et al.

ACS BIOMATERIALS SCIENCE & ENGINEERING (2020)

Proceedings Paper Biochemical Research Methods

Chemical-protein Interaction Extraction via ChemicalBERT and Attention Guided Graph Convolutional Networks in Parallel

Lei Qin et al.

2020 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (2020)

Review Chemistry, Multidisciplinary

Additive Manufacturing Approaches for Hydroxyapatite-Reinforced Composites

Mario Milazzo et al.

ADVANCED FUNCTIONAL MATERIALS (2019)

Article Multidisciplinary Sciences

rawMSA: End-to-end Deep Learning using raw Multiple Sequence Alignments

Claudio Mirabello et al.

PLOS ONE (2019)

Review Chemistry, Multidisciplinary

The Collagen Suprafamily: From Biosynthesis to Advanced Biomaterial Development

Anna Sorushanova et al.

ADVANCED MATERIALS (2019)

Review Chemistry, Multidisciplinary

Collagen Structure-Function Relationships from Solid-State NMR Spectroscopy

Ieva Goldberga et al.

ACCOUNTS OF CHEMICAL RESEARCH (2018)

Article Biophysics

Single-Molecule Assay for Proteolytic Susceptibility: Force-Induced Collagen Destabilization

Michael W. H. Kirkness et al.

BIOPHYSICAL JOURNAL (2018)

Article Biochemistry & Molecular Biology

Collagen Gly missense mutations: Effect of residue identity on collagen structure and integrin binding

Yimin Qiu et al.

JOURNAL OF STRUCTURAL BIOLOGY (2018)

Article Multidisciplinary Sciences

Computational Protein Design with Deep Learning Neural Networks

Jingxue Wang et al.

SCIENTIFIC REPORTS (2018)

Article Biochemistry & Molecular Biology

Non-linearity of the collagen triple helix in solution and implications for collagen function

Kenneth T. Walker et al.

BIOCHEMICAL JOURNAL (2017)

Article Nanoscience & Nanotechnology

Collagen Gels with Different Fibrillar Microarchitectures Elicit Different Cellular Responses

Jing Xie et al.

ACS APPLIED MATERIALS & INTERFACES (2017)

Article Chemistry, Multidisciplinary

Dissociated and Reconstituted Cartilage Microparticles in Densified Collagen Induce Local hMSC Differentiation

Tyler Novak et al.

ADVANCED FUNCTIONAL MATERIALS (2016)

Article Biochemistry & Molecular Biology

Bacterial collagen-like proteins that form triple-helical structures

Zhuoxin Yu et al.

JOURNAL OF STRUCTURAL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Structural Insights into Charge Pair Interactions in Triple Helical Collagen-like Proteins

Jorge A. Fallas et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2012)

Article Biochemistry & Molecular Biology

Viscoelastic properties of model segments of collagen molecules

Alfonso Gautieri et al.

MATRIX BIOLOGY (2012)

Review Chemistry, Physical

Collagen-Based Biomaterials for Tissue Engineering Applications

Remi Parenteau-Bareil et al.

MATERIALS (2010)

Review Biochemistry & Molecular Biology

Collagen Structure and Stability

Matthew D. Shoulders et al.

ANNUAL REVIEW OF BIOCHEMISTRY (2009)

Article Biophysics

Mechanical properties of native and cross-linked type I collagen fibrils

Lanti Yang et al.

BIOPHYSICAL JOURNAL (2008)

Article Biophysics

Stress-strain experiments on individual collagen fibrils

Zhilei L. Shen et al.

BIOPHYSICAL JOURNAL (2008)

Article Biochemistry & Molecular Biology

Triple-helical peptides: An approach to collagen conformation, stability, and self-association

Barbara Brodsky et al.

BIOPOLYMERS (2008)

Article Biochemistry & Molecular Biology

Mechanism of stabilization of a bacterial collagen triple helix in the absence of hydroxyproline

Angela Mohs et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2007)

Article Biophysics

Entropic elasticity controls nanomechanics of single tropocollagen molecules

Markus J. Buehler et al.

BIOPHYSICAL JOURNAL (2007)

Article Biotechnology & Applied Microbiology

Predicting protein function by machine learning on amino acid sequences - a critical evaluation

Ali Al-Shahib et al.

BMC GENOMICS (2007)

Article Biochemistry & Molecular Biology

Micromechanical testing of individual collagen fibrils

Joost A. J. van der Rijt et al.

MACROMOLECULAR BIOSCIENCE (2006)

Article Multidisciplinary Sciences

Nature designs tough collagen: Explaining the nanostructure of collagen fibrils

Markus J. Buehler

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Materials Science, Multidisciplinary

Atomistic and continuum modeling of mechanical properties of collagen: Elasticity, fracture, and self-assembly

Markus J. Buehler

JOURNAL OF MATERIALS RESEARCH (2006)

Article Chemistry, Multidisciplinary

Reciprocity of steric and stereoelectronic effects in the collagen triple helix

Matthew D. Shoulders et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Multidisciplinary Sciences

Microfibrillar structure of type I collagen in situ

Joseph P. R. O. Orgel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Review Chemistry, Multidisciplinary

Scalable molecular dynamics with NAMD

JC Phillips et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Article Biochemistry & Molecular Biology

Prediction of collagen stability from amino acid sequence

AV Persikov et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2005)

Review Biochemistry & Molecular Biology

Collagen structure: The Madras triple helix and the current scenario

A Bhattacharjee et al.

IUBMB LIFE (2005)

Article Engineering, Biomedical

Mechanistic aspects of fracture and R-curve behavior in human cortical bone

RK Nalla et al.

BIOMATERIALS (2005)

Article Biochemistry & Molecular Biology

Equilibrium thermal transitions of collagen model peptides

AV Persikov et al.

PROTEIN SCIENCE (2004)

Article Materials Science, Multidisciplinary

Characteristic dimensions and the micro-mechanisms of fracture and fatigue in 'nano' and 'bio' materials

RO Ritchie et al.

INTERNATIONAL JOURNAL OF FRACTURE (2004)

Article Biochemical Research Methods

An interactive triple-helical collagen builder

JK Rainey et al.

BIOINFORMATICS (2004)

Article Chemistry, Multidisciplinary

Effect of 3-hydroxyproline residues on collagen stability

CL Jenkins et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

Article Biology

Viscoelastic properties of collagen: synchrotron radiation investigations and structural model

R Puxkandl et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2002)

Article Biochemistry & Molecular Biology

Peptide investigations of pairwise interactions in the collagen triple-helix

AV Persikov et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Review Pharmacology & Pharmacy

Biomedical applications of collagen

CH Lee et al.

INTERNATIONAL JOURNAL OF PHARMACEUTICS (2001)

Article Chemistry, Multidisciplinary

Conformational stability of collagen relies on a stereoelectronic effect

LE Bretscher et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)

Article Biochemistry & Molecular Biology

Amino acid propensities for the collagen triple-helix

AV Persikov et al.

BIOCHEMISTRY (2000)