Simulating the mechanisms of life through the lens of the virtual world

Authors: Snegirev, Nadia

Source: University of Auckland scientific, Oct 2023; v.3 n.4:p.19-22,26-27

Access URL: https://ndhadeliver.natlib.govt.nz/delivery/DeliveryManagerServlet?dps_pid=IE90601969

Template-based prediction of protein structure with deep learning

Authors: Zhang, Haicang, Shen, Yufeng

Subject Terms: Deep learning (Machine learning), Proteins--Structure--Computer simulation, Neural networks (Computer science)

Availability: https://doi.org/10.7916/mq98-nm22

Template-based prediction of protein structure with deep learning

Authors: Haicang Zhang, Yufeng Shen

Source: BMC Genomics
BMC Genomics, Vol 21, Iss S11, Pp 1-9 (2020)

Subject Terms: 0301 basic medicine, Deep learning (Machine learning), Protein Conformation, 0206 medical engineering, Methodology, Proteins, Deep learning, 02 engineering and technology, QH426-470, Protein threading, Proteins--Structure--Computer simulation, Neural networks (Computer science), 03 medical and health sciences, Deep Learning, Protein structure prediction, Sequence Analysis, Protein, Genetics, Databases, Protein, Deep residual neural network, TP248.13-248.65, Algorithms, Software, Biotechnology

Access URL: https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-020-07249-8
https://pubmed.ncbi.nlm.nih.gov/33372607
https://doaj.org/article/41b2613251c8434e969052e8ca136cf4

A computational framework for parallelised protein folding simulation and the investigation of protein stability

Authors: Koh, Tammara Poa Siang

Contributors: Tromp, Gerard, Patterton, Hugh George, Stellenbosch University. Faculty of Science. Centre for Bioinformatics & Computational Biology.

Subject Terms: Proteins -- Structure -- Computer simulation, Computational biology, Protein folding -- Computer simulation, Molecular dynamics -- Computer simulation, UCTD

File Description: x, 95 pages : illustrations; application/pdf

Relation: https://scholar.sun.ac.za/handle/10019.1/132586

Availability: https://scholar.sun.ac.za/handle/10019.1/132586

Investigating mitochondrial DNA mutations driving dysfunction and intervertebral disc degeneration

Authors: Collins, Megan

Contributors: Pearce, Brendon Clive, Stellenbosch University. Faculty of Agrisciences. Dept. of Genetics.

Subject Terms: Mitochondrial DNA, Mitochondrial pathology -- Genetic aspects, Proteins -- Structure -- Computer simulation, Mutation (Biology) -- Data processing, Transfer RNA, UCTD

File Description: xii, 156 pages : illustrations; application/pdf

Relation: https://scholar.sun.ac.za/handle/10019.1/132107

Availability: https://scholar.sun.ac.za/handle/10019.1/132107

Empirical study of deep neural network architectures for protein secondary structure prediction

Authors: Du, Ming

Contributors: Shang, Yi, 1967

Subject Terms: Proteins -- Structure -- Computer simulation

Access URL: https://mospace.umsystem.edu/xmlui/bitstream/10355/62043/1/public.pdf

Loop Prediction and Homology Modeling with High Resolution

Authors: Xu, Tianchuan

Subject Terms: Bioinformatics, Proteins--Structure--Computer simulation, Homology (Biology), Sequence alignment (Bioinformatics)

Availability: https://doi.org/10.7916/d8-1dqz-y485

A Metaheuristic Approach to Protein Structure Prediction

Authors: Nanda Dulal Jana, Swagatam Das, Jaya Sil

Resource Type: eBook.

Subjects: Mathematical models, Computer simulation, Digital computer simulation, Proteins--Structure--Mathematical models, Proteins--Structure--Computer simulation, Proteins--Conformation

Categories: COMPUTERS / Artificial Intelligence / General, SCIENCE / Chemistry / Organic, SCIENCE / System Theory, TECHNOLOGY & ENGINEERING / Engineering (General)

From Protein Structure to Function with Bioinformatics

Authors: Daniel J. Rigden

Resource Type: eBook.

Subjects: Proteins--Structure, Proteins--Structure--Research--Methodology, Proteins--Structure-activity relationships--Research--Methodology, Proteins--Structure--Computer simulation, Computational biology, Bioinformatics

Categories: SCIENCE / Life Sciences / Molecular Biology, COMPUTERS / Data Science / Bioinformatics, MEDICAL / Research, SCIENCE / Life Sciences / Biochemistry, SCIENCE / Life Sciences / Biology, SCIENCE / Research & Methodology

Development and application of efficient and accurate free-energy models and methodologies for high-throughput computational protein design

Authors: Michael, Eleni M.

Contributors: Archontis, Georgios, Αρχοντής, Γεώργιος, Σκουρτής, Σπύρος, Πτωχός, Φώτιος, Λεοντίδης, Επαμεινώνδας, Skourtis, Spiros, Ptochos, Photios, Leontidis, Epameinondas, Stote, Roland, Πανεπιστήμιο Κύπρου, Σχολή Θετικών και Εφαρμοσμένων Επιστημών, Τμήμα Φυσικής, University of Cyprus, Faculty of Pure and Applied Sciences, Department of Physics, Archontis, Georgios [0000-0002-7750-8641]

Subject Terms: PROTEIN DESIGN, COMPUTER SIMULATION, Proteins -- Structure -- Computer simulation, LIGAND DESIGN, FULL PROTEIN REDESIGN, FOCAL ADHESION KINASE, IMPLICIT SOLVENT, ΠΛΗΡΗΣ ΕΠΑΝΑΣΧΕΔΙΑΣΜΟΣ ΠΡΩΤΕΙΝΩΝ, Molecular dynamics, ΣΧΕΔΙΑΣΜΟΣ ΠΡΩΤΕΙΝΩΝ, ΜΟΤΙΒΑ LD, ΣΧΕΤΙΚΗ ΕΝΕΡΓΕΙΑ ΣΥΝΔΕΣΗΣ, ΣΧΕΔΙΑΣΜΟΣ ΠΕΠΤΙΔΙΩΝ, ΥΠΟΛΟΓΙΣΜΟΙ ΕΛΕΥΘΕΡΗΣ ΕΝΕΡΓΕΙΑΣ, MONTE CARLO, XPLOR PROGRAM, ΓΕΝΙΚΕΥΜΕΝΟ ΜΟΝΤΕΛΟ BORN, ΤΙΜΗ PH, RELATIVE BINDING FREE ENERGY, ΠΡΟΓΡΑΜΜΑ XPLOR, LD MOTIFS, Ligands (Biochemistry), ΜΟΡΙΑΚΗ ΔΥΝΑΜΙΚΗ, FREE ENERGY CALCULATIONS, Computer simulation, ΥΠΟΛΟΓΙΣΤΙΚΗ ΠΡΟΣΟΜΟΙΩΣΗ, ΜΟΝΤΕ ΚΑΡΛΟ, PH VALUE, MOLECULAR DYNAMICS, Protein engineering, ΕΜΜΕΣΗ ΑΝΑΠΑΡΑΣΤΑΣΗ ΔΙΑΛΥΤΗ, GENERALIZED BORN MODEL, ΚΙΝΑΣΗ ΕΣΤΙΑΚΗΣ ΠΡΟΣΚΟΛΛΗΣΗΣ

File Description: xiii, 277 p. : col. ill., diagrs., tables; 30 cm.

Access URL: http://gnosis.library.ucy.ac.cy/handle/7/64835

A meta-heuristic optimization tool for simplified protein structure prediction

Contributors: Lakha, Gurpreet Singh (Author), Aravind, Alex (Thesis advisor), University of Northern British Columbia College of Science and Management (Degree granting institution), Jones, George (Degree committee member), Rader, Stephen (Degree committee member)

Subject Terms: Proteins--Structure--Computer simulation, Proteins--Structure--Mathematical models

File Description: electronic; 1 online resource (100 pages)

Relation: https://arcabc.ca/islandora/object/unbc%3A58945; unbc:58945

Availability: https://arcabc.ca/islandora/object/unbc%3A58945
https://doi.org/10.24124/2019/58945

Improving oral drug delivery: computational studies of proton dependent oligopeptide transporters

Authors: Samsudin, M

Contributors: Fowler, P, Sansom, M

Subject Terms: Peptides--Physiological transport, Drugs--Bioavailability, Molecular dynamics--Computer simulation, Gibbs' free energy, Beta lactam antibiotics, Ligand binding (Biochemistry), Proteins--Structure--Computer simulation

Availability: https://doi.org/10.5287/ora-ny5va7pbk
https://ora.ox.ac.uk/objects/uuid:ce400815-fd55-49dc-8f43-3f620d3e132e

Protein Folding in Silico : Protein Folding Versus Protein Structure Prediction

Authors: Irena Roterman-Konieczna

Resource Type: eBook.

Subjects: Mathematical models, Protein folding, Proteins--Structure--Computer simulation

Categories: SCIENCE / Life Sciences / Biochemistry

Effect of the ligand in the Modeling the 3d structure of the m3 muscarinic receptor

Authors: Rasaeifar, Bahareh

Contributors: Pérez González, Juan Jesús

Subject Terms: Àrees temàtiques de la UPC::Enginyeria química::Biotecnologia, Ligand binding (Biochemistry) -- Computer simulation, G proteins -- Structure -- Computer simulation, Three-dimensional display systems, Lligands (Bioquímica) -- Simulació per ordinador, Proteïnes G -- Estructura -- Simulació per ordinador, Visualització tridimensional (Informàtica)

File Description: application/pdf

Relation: https://hdl.handle.net/2099.1/21428

Availability: https://hdl.handle.net/2099.1/21428

Introduction to Protein Structure Prediction : Methods and Algorithms

Authors: Huzefa Rangwala, George Karypis

Resource Type: eBook.

Subjects: Molecular structure, Proteins--Conformation, Proteins--Structure--Mathematical models, Proteins--Structure--Computer simulation, Mathematical models

Categories: SCIENCE / Life Sciences / Molecular Biology

Etude bioinformatique de la stabilité thermique des protéines: conception de potentiels statistiques dépendant de la température et développement d'approches prédictives ; Bioinformatic study of protein thermal stability: development of temperature dependent statistical potentials and design of predictive approaches

Authors: Folch, Benjamin

Contributors: Rooman, Marianne, Bogaerts, Philippe, Lenaerts, Tom, Gilis, Dimitri, Wintjens, René, Guerois, Raphaël, Biot, Christophe

Subject Terms: Agronomie générale, Sciences de l'ingénieur, Proteins -- Structure -- Computer simulation, Proteins -- Conformation, Bioinformatics, Protéines -- Structure -- Simulation par ordinateur, Protéines -- Conformation, Bio-informatique, température de fusion/melting temperature, thermostabilité/thermostability, interaction protéiques/protein interactions, stabilité thermodynamique/thermodynamic stability

File Description: 1 v.; 12 full-text file(s): application/pdf | application/pdf | application/pdf | application/pdf | application/pdf | application/pdf | application/pdf | application/pdf | application/pdf | application/pdf | application/pdf | application/pdf

Relation: local/ulbcat.ulb.ac.be:893835

Availability: https://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210106
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/11/99427dca-c96c-4812-9e5d-205c5d833af8.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/2/04fc4c01-f8f3-42d2-b215-84ceaa4aa87f.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/14/f03c3666-ea67-4234-99ad-9669e0ce521b.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/1/41ffaf7a-fa48-4862-a812-bedb5904aa71.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/5/133a059e-abde-413b-bade-6eee5931cb29.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/6/880c74ca-39e4-49ee-81ae-bcedb4bc8daf.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/7/7b23c46a-812b-4ea4-a013-46c5b5c5b2d7.txt
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https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/9/a9eb0410-b41e-47b5-9fc7-f654e5a1c665.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/3/273b1dd3-70db-4b73-a695-9d210bf4e3e5.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/10/bc20d7f4-79eb-49e1-ac97-30be587b3ec8.txt

From Protein Structure to Function with Bioinformatics

Authors: Daniel John Rigden

Resource Type: eBook.

Subjects: Bioinformatics, Computational biology, Proteins--Structure, Proteins--Structure--Computer simulation, Amino acid sequence

Categories: SCIENCE / Life Sciences / Molecular Biology, COMPUTERS / Data Science / Bioinformatics, MEDICAL / Research, SCIENCE / Life Sciences / Biochemistry, SCIENCE / Life Sciences / Biology, SCIENCE / Research & Methodology, SCIENCE / Life Sciences / General

Computational Structural Biology : Methods and Applications

Authors: Torsten Schwede, Manuel C Peitsch

Resource Type: eBook.

Subjects: Computational biology, Bioinformatics, Proteins--Conformation, Protein folding--Mathematical models, Proteins--Structure--Computer simulation, Protein folding--Computer simulation, Proteins--Structure--Mathematical models, Drugs--Design, RNA

Categories: SCIENCE / Life Sciences / General, SCIENCE / Biotechnology

Lecture Notes on Computational Structural Biology

Authors: Zhijun Wu

Resource Type: eBook.

Subjects: Proteins--Structure--Mathematical models, Protein folding--Mathematical models, Proteins--Structure--Computer simulation, Protein folding--Computer simulation, Computational biology, Bioinformatics

Categories: SCIENCE / Life Sciences / General, SCIENCE / Biotechnology

Etude bioinformatique de la stabilité thermique des protéines: conception de potentiels statistiques dépendant de la température et développement d'approches prédictives

Authors: Folch, Benjamin

Contributors: Rooman, Marianne, Bogaerts, Philippe, Lenaerts, Tom, Gilis, Dimitri, Wintjens, René, Guerois, Raphaël, Biot, Christophe

Subject Terms: thermostabilité/thermostability, interaction protéiques/protein interactions, Proteins -- Structure -- Computer simulation, Bioinformatics, Agronomie générale, température de fusion/melting temperature, Protéines -- Conformation, Bio-informatique, Sciences de l'ingénieur, Protéines -- Structure -- Simulation par ordinateur, stabilité thermodynamique/thermodynamic stability, Proteins -- Conformation

File Description: 12 full-text file(s): application/pdf; application/pdf

Access URL: https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/3/273b1dd3-70db-4b73-a695-9d210bf4e3e5.txt
http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210106
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/7/7b23c46a-812b-4ea4-a013-46c5b5c5b2d7.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/9/a9eb0410-b41e-47b5-9fc7-f654e5a1c665.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/5/133a059e-abde-413b-bade-6eee5931cb29.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/14/f03c3666-ea67-4234-99ad-9669e0ce521b.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/10/bc20d7f4-79eb-49e1-ac97-30be587b3ec8.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/6/880c74ca-39e4-49ee-81ae-bcedb4bc8daf.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/11/99427dca-c96c-4812-9e5d-205c5d833af8.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/8/75d6b5b8-a978-4ea4-add5-0da7b49f35f5.txt
https://dipot.ulb.ac.be/dspace/bitstream/2013/210106/1/41ffaf7a-fa48-4862-a812-bedb5904aa71.txt
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