Structural bioinformatics (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Structural bioinformatics" in English language version.

refsWebsite

Global rank English rank

20nih.gov

4^th place

18doi.org

2^nd place

4semanticscholar.org

11^th place

8^th place

3worldcat.org

5^th place

3wwpdb.org

low place

2web.archive.org

1^st place

2fccc.edu

low place

1books.google.com

3^rd place

1ufmg.br

8,008^th place

low place

1acm.org

1,185^th place

840^th place

1embrapa.br

6,067^th place

low place

1rutgers.edu

1,999^th place

1,355^th place

1cam.ac.uk

670^th place

480^th place

1uu.se

3,805^th place

3,371^st place

1predictioncenter.org

low place

1sbkb.org

low place

1ebi.ac.uk

5,849^th place

7,886^th place

1sciencedaily.com

993^rd place

920^th place

1ibb.waw.pl

low place

1harvard.edu

18^th place

17^th place

1ukm.my

low place

1chemcomp.com

low place

1ball-project.org

low place

1pymol.org

low place

1uiuc.edu

3,087^th place

2,519^th place

1gromacs.org

low place

1lammps.org

low place

1iastate.edu

2,548^th place

1,587^th place

acm.org

dl.acm.org

Martins PM, Mayrink VD, de Silveira S, da Silveira CH, de Lima LH, de Melo-Minardi RC (2018). "How to compute protein residue contacts more accurately?". Proceedings of the 33rd Annual ACM Symposium on Applied Computing. Pau, France: ACM Press. pp. 60–67. doi:10.1145/3167132.3167136. ISBN 978-1-4503-5191-1. S2CID 49562347.

ball-project.org

BALLView

books.google.com

Gu J, Bourne PE (2009-03-16). Structural Bioinformatics. John Wiley & Sons. ISBN 978-0-470-18105-8.

cam.ac.uk

scop.mrc-lmb.cam.ac.uk

"SCOP: Structural Classification of Proteins". 2007-09-11. Archived from the original on 2007-09-11. Retrieved 2020-04-13.

chemcomp.com

doi.org

Kocincová L, Jarešová M, Byška J, Parulek J, Hauser H, Kozlíková B (February 2017). "Comparative visualization of protein secondary structures". BMC Bioinformatics. 18 (Suppl 2): 23. doi:10.1186/s12859-016-1449-z. PMC 5333176. PMID 28251875.
Shi M, Gao J, Zhang MQ (July 2017). "Web3DMol: interactive protein structure visualization based on WebGL". Nucleic Acids Research. 45 (W1): W523–W527. doi:10.1093/nar/gkx383. PMC 5570197. PMID 28482028.
Stanfield RL, Wilson IA (February 1995). "Protein-peptide interactions". Current Opinion in Structural Biology. 5 (1): 103–13. doi:10.1016/0959-440X(95)80015-S. PMID 7773739.
Klebe G (2015). "Protein–Ligand Interactions as the Basis for Drug Action". In Scapin G, Patel D, Arnold E (eds.). Drug Design. NATO Science for Peace and Security Series A: Chemistry and Biology. Dordrecht: Springer. pp. 83–92. doi:10.1007/978-3-642-17907-5_4. ISBN 978-3-642-17906-8.
Martins PM, Mayrink VD, de Silveira S, da Silveira CH, de Lima LH, de Melo-Minardi RC (2018). "How to compute protein residue contacts more accurately?". Proceedings of the 33rd Annual ACM Symposium on Applied Computing. Pau, France: ACM Press. pp. 60–67. doi:10.1145/3167132.3167136. ISBN 978-1-4503-5191-1. S2CID 49562347.
da Silveira CH, Pires DE, Minardi RC, Ribeiro C, Veloso CJ, Lopes JC, et al. (February 2009). "Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins" (PDF). Proteins. 74 (3): 727–43. doi:10.1002/prot.22187. PMID 18704933. S2CID 1208256.
Ilyin VA, Abyzov A, Leslin CM (July 2004). "Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point". Protein Science. 13 (7): 1865–74. doi:10.1110/ps.04672604. PMC 2279929. PMID 15215530.
Pires DE, de Melo-Minardi RC, dos Santos MA, da Silveira CH, Santoro MM, Meira W (December 2011). "Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns". BMC Genomics. 12 Suppl 4 (S4): S12. doi:10.1186/1471-2164-12-S4-S12. PMC 3287581. PMID 22369665.
Mariano DC, Santos LH, Machado KD, Werhli AV, de Lima LH, de Melo-Minardi RC (January 2019). "A Computational Method to Propose Mutations in Enzymes Based on Structural Signature Variation (SSV)". International Journal of Molecular Sciences. 20 (2): 333. doi:10.3390/ijms20020333. PMC 6359350. PMID 30650542.
Kaczanowski S, Zielenkiewicz P (March 2010). "Why similar protein sequences encode similar three-dimensional structures?" (PDF). Theoretical Chemistry Accounts. 125 (3–6): 643–650. doi:10.1007/s00214-009-0656-3. ISSN 1432-881X. S2CID 95593331.
Chothia C, Lesk AM (April 1986). "The relation between the divergence of sequence and structure in proteins". The EMBO Journal. 5 (4): 823–6. doi:10.1002/j.1460-2075.1986.tb04288.x. PMC 1166865. PMID 3709526.
"So much more to know". Science. 309 (5731): 78–102. July 2005. doi:10.1126/science.309.5731.78b. PMID 15994524.
Webb B, Sali A (September 2014). "Comparative Protein Structure Modeling Using MODELLER". Current Protocols in Bioinformatics. 47 (1): 5.6.1–32. doi:10.1002/0471250953.bi0506s47. PMC 4186674. PMID 25199792.
Dhasmana A, Raza S, Jahan R, Lohani M, Arif JM (2019-01-01). "Chapter 19 - High-Throughput Virtual Screening (HTVS) of Natural Compounds and Exploration of Their Biomolecular Mechanisms: An In Silico Approach". In Ahmad Khan MS, Ahmad I, Chattopadhyay D (eds.). New Look to Phytomedicine. Academic Press. pp. 523–548. doi:10.1016/b978-0-12-814619-4.00020-3. ISBN 978-0-12-814619-4. S2CID 69534557.
Wermuth CG, Villoutreix B, Grisoni S, Olivier A, Rocher JP (January 2015). "Strategies in the search for new lead compounds or original working hypotheses.". In Wermuth CG, Aldous D, Raboisson P, Rognan D (eds.). The practice of Medicinal Chemistry. Academic Press. pp. 73–99. doi:10.1016/B978-0-12-417205-0.00004-3. ISBN 978-0-12-417205-0.
Costa LS, Mariano DC, Rocha RE, Kraml J, Silveira CH, Liedl KR, et al. (September 2019). "Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases". Molecules. 24 (18): 3215. doi:10.3390/molecules24183215. PMC 6766793. PMID 31487855.
Alder BJ, Wainwright TE (August 1959). "Studies in Molecular Dynamics. I. General Method". The Journal of Chemical Physics. 31 (2): 459–466. Bibcode:1959JChPh..31..459A. doi:10.1063/1.1730376. ISSN 0021-9606.
Yousif, Ragheed Hussam (2020). "Exploring the Molecular Interactions between Neoculin and the Human Sweet Taste Receptors through Computational Approaches" (PDF). Sains Malaysiana. 49 (3): 517–525. doi:10.17576/jsm-2020-4903-06.

ebi.ac.uk

alphafold.ebi.ac.uk

"AlphaFold".

embrapa.br

ainfo.cnptia.embrapa.br

da Silveira CH, Pires DE, Minardi RC, Ribeiro C, Veloso CJ, Lopes JC, et al. (February 2009). "Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins" (PDF). Proteins. 74 (3): 727–43. doi:10.1002/prot.22187. PMID 18704933. S2CID 1208256.

fccc.edu

dunbrack.fccc.edu

":: Dunbrack Lab". dunbrack.fccc.edu. Retrieved 2020-04-13.

dunbrack2.fccc.edu

"Protein Common Interface Database". dunbrack2.fccc.edu. Retrieved 2020-04-13.

gromacs.org

Gromacs

harvard.edu

ui.adsabs.harvard.edu

Alder BJ, Wainwright TE (August 1959). "Studies in Molecular Dynamics. I. General Method". The Journal of Chemical Physics. 31 (2): 459–466. Bibcode:1959JChPh..31..459A. doi:10.1063/1.1730376. ISSN 0021-9606.

iastate.edu

msg.chem.iastate.edu

GAMESS

ibb.waw.pl

eprints.ibb.waw.pl

Kaczanowski S, Zielenkiewicz P (March 2010). "Why similar protein sequences encode similar three-dimensional structures?" (PDF). Theoretical Chemistry Accounts. 125 (3–6): 643–650. doi:10.1007/s00214-009-0656-3. ISSN 1432-881X. S2CID 95593331.

lammps.org

LAMMPS

nih.gov

pubmed.ncbi.nlm.nih.gov

Kocincová L, Jarešová M, Byška J, Parulek J, Hauser H, Kozlíková B (February 2017). "Comparative visualization of protein secondary structures". BMC Bioinformatics. 18 (Suppl 2): 23. doi:10.1186/s12859-016-1449-z. PMC 5333176. PMID 28251875.
Shi M, Gao J, Zhang MQ (July 2017). "Web3DMol: interactive protein structure visualization based on WebGL". Nucleic Acids Research. 45 (W1): W523–W527. doi:10.1093/nar/gkx383. PMC 5570197. PMID 28482028.
Stanfield RL, Wilson IA (February 1995). "Protein-peptide interactions". Current Opinion in Structural Biology. 5 (1): 103–13. doi:10.1016/0959-440X(95)80015-S. PMID 7773739.
da Silveira CH, Pires DE, Minardi RC, Ribeiro C, Veloso CJ, Lopes JC, et al. (February 2009). "Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins" (PDF). Proteins. 74 (3): 727–43. doi:10.1002/prot.22187. PMID 18704933. S2CID 1208256.
Ilyin VA, Abyzov A, Leslin CM (July 2004). "Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point". Protein Science. 13 (7): 1865–74. doi:10.1110/ps.04672604. PMC 2279929. PMID 15215530.
Pires DE, de Melo-Minardi RC, dos Santos MA, da Silveira CH, Santoro MM, Meira W (December 2011). "Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns". BMC Genomics. 12 Suppl 4 (S4): S12. doi:10.1186/1471-2164-12-S4-S12. PMC 3287581. PMID 22369665.
Mariano DC, Santos LH, Machado KD, Werhli AV, de Lima LH, de Melo-Minardi RC (January 2019). "A Computational Method to Propose Mutations in Enzymes Based on Structural Signature Variation (SSV)". International Journal of Molecular Sciences. 20 (2): 333. doi:10.3390/ijms20020333. PMC 6359350. PMID 30650542.
Chothia C, Lesk AM (April 1986). "The relation between the divergence of sequence and structure in proteins". The EMBO Journal. 5 (4): 823–6. doi:10.1002/j.1460-2075.1986.tb04288.x. PMC 1166865. PMID 3709526.
"So much more to know". Science. 309 (5731): 78–102. July 2005. doi:10.1126/science.309.5731.78b. PMID 15994524.
Webb B, Sali A (September 2014). "Comparative Protein Structure Modeling Using MODELLER". Current Protocols in Bioinformatics. 47 (1): 5.6.1–32. doi:10.1002/0471250953.bi0506s47. PMC 4186674. PMID 25199792.
Costa LS, Mariano DC, Rocha RE, Kraml J, Silveira CH, Liedl KR, et al. (September 2019). "Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases". Molecules. 24 (18): 3215. doi:10.3390/molecules24183215. PMC 6766793. PMID 31487855.

ncbi.nlm.nih.gov

Kocincová L, Jarešová M, Byška J, Parulek J, Hauser H, Kozlíková B (February 2017). "Comparative visualization of protein secondary structures". BMC Bioinformatics. 18 (Suppl 2): 23. doi:10.1186/s12859-016-1449-z. PMC 5333176. PMID 28251875.
Shi M, Gao J, Zhang MQ (July 2017). "Web3DMol: interactive protein structure visualization based on WebGL". Nucleic Acids Research. 45 (W1): W523–W527. doi:10.1093/nar/gkx383. PMC 5570197. PMID 28482028.
"Macromolecular Structures Resource Group". www.ncbi.nlm.nih.gov. Retrieved 2020-04-13.
Ilyin VA, Abyzov A, Leslin CM (July 2004). "Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point". Protein Science. 13 (7): 1865–74. doi:10.1110/ps.04672604. PMC 2279929. PMID 15215530.
Pires DE, de Melo-Minardi RC, dos Santos MA, da Silveira CH, Santoro MM, Meira W (December 2011). "Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns". BMC Genomics. 12 Suppl 4 (S4): S12. doi:10.1186/1471-2164-12-S4-S12. PMC 3287581. PMID 22369665.
Mariano DC, Santos LH, Machado KD, Werhli AV, de Lima LH, de Melo-Minardi RC (January 2019). "A Computational Method to Propose Mutations in Enzymes Based on Structural Signature Variation (SSV)". International Journal of Molecular Sciences. 20 (2): 333. doi:10.3390/ijms20020333. PMC 6359350. PMID 30650542.
Chothia C, Lesk AM (April 1986). "The relation between the divergence of sequence and structure in proteins". The EMBO Journal. 5 (4): 823–6. doi:10.1002/j.1460-2075.1986.tb04288.x. PMC 1166865. PMID 3709526.
Webb B, Sali A (September 2014). "Comparative Protein Structure Modeling Using MODELLER". Current Protocols in Bioinformatics. 47 (1): 5.6.1–32. doi:10.1002/0471250953.bi0506s47. PMC 4186674. PMID 25199792.
Costa LS, Mariano DC, Rocha RE, Kraml J, Silveira CH, Liedl KR, et al. (September 2019). "Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases". Molecules. 24 (18): 3215. doi:10.3390/molecules24183215. PMC 6766793. PMID 31487855.

predictioncenter.org

"Home - Prediction Center". www.predictioncenter.org. Retrieved 2020-04-13.

pymol.org

PyMOL

rutgers.edu

ndbserver.rutgers.edu

"Nucleic Acid Database (NDB)". ndbserver.rutgers.edu. Retrieved 2020-04-13.

sbkb.org

"Structural Biology KnowlegebaseSBKB - SBKB". sbkb.org. Retrieved 2020-04-13.

sciencedaily.com

"Structural alignment (genomics)". ScienceDaily. Retrieved 2020-02-26.

semanticscholar.org

api.semanticscholar.org

Martins PM, Mayrink VD, de Silveira S, da Silveira CH, de Lima LH, de Melo-Minardi RC (2018). "How to compute protein residue contacts more accurately?". Proceedings of the 33rd Annual ACM Symposium on Applied Computing. Pau, France: ACM Press. pp. 60–67. doi:10.1145/3167132.3167136. ISBN 978-1-4503-5191-1. S2CID 49562347.
da Silveira CH, Pires DE, Minardi RC, Ribeiro C, Veloso CJ, Lopes JC, et al. (February 2009). "Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins" (PDF). Proteins. 74 (3): 727–43. doi:10.1002/prot.22187. PMID 18704933. S2CID 1208256.
Kaczanowski S, Zielenkiewicz P (March 2010). "Why similar protein sequences encode similar three-dimensional structures?" (PDF). Theoretical Chemistry Accounts. 125 (3–6): 643–650. doi:10.1007/s00214-009-0656-3. ISSN 1432-881X. S2CID 95593331.
Dhasmana A, Raza S, Jahan R, Lohani M, Arif JM (2019-01-01). "Chapter 19 - High-Throughput Virtual Screening (HTVS) of Natural Compounds and Exploration of Their Biomolecular Mechanisms: An In Silico Approach". In Ahmad Khan MS, Ahmad I, Chattopadhyay D (eds.). New Look to Phytomedicine. Academic Press. pp. 523–548. doi:10.1016/b978-0-12-814619-4.00020-3. ISBN 978-0-12-814619-4. S2CID 69534557.

ufmg.br

proteus.dcc.ufmg.br

"Proteus | PROTein Engineering Supporter |". proteus.dcc.ufmg.br. Retrieved 2020-02-26.

uiuc.edu

ks.uiuc.edu

ukm.my

Yousif, Ragheed Hussam (2020). "Exploring the Molecular Interactions between Neoculin and the Human Sweet Taste Receptors through Computational Approaches" (PDF). Sains Malaysiana. 49 (3): 517–525. doi:10.17576/jsm-2020-4903-06.

uu.se

eds.bmc.uu.se

"EDS - Uppsala Electron Density Server". eds.bmc.uu.se. Retrieved 2020-04-13.

web.archive.org

"SCOP: Structural Classification of Proteins". 2007-09-11. Archived from the original on 2007-09-11. Retrieved 2020-04-13.
STRIDE

worldcat.org

search.worldcat.org

Gu J, Bourne PE (2011). Structural Bioinformatics (2nd ed.). Hoboken: John Wiley & Sons. ISBN 978-1-118-21056-7. OCLC 778339075.
Kaczanowski S, Zielenkiewicz P (March 2010). "Why similar protein sequences encode similar three-dimensional structures?" (PDF). Theoretical Chemistry Accounts. 125 (3–6): 643–650. doi:10.1007/s00214-009-0656-3. ISSN 1432-881X. S2CID 95593331.
Alder BJ, Wainwright TE (August 1959). "Studies in Molecular Dynamics. I. General Method". The Journal of Chemical Physics. 31 (2): 459–466. Bibcode:1959JChPh..31..459A. doi:10.1063/1.1730376. ISSN 0021-9606.

wwpdb.org

mmcif.wwpdb.org

"PDBx/mmCIF General FAQ". mmcif.wwpdb.org. Retrieved 2020-02-26.
"PDBx/mmCIF Dictionary Resources". mmcif.wwpdb.org. Retrieved 2020-02-26.

wwpdb.org

wwPDB.org. "wwPDB: File Formats and the PDB". www.wwpdb.org. Retrieved 2020-02-26.