Macromolecular docking (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Macromolecular docking" in English language version.

refsWebsite

Global rank English rank

32nih.gov

4^th place

22doi.org

2^nd place

6semanticscholar.org

11^th place

8^th place

2harvard.edu

18^th place

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1handle.net

102^nd place

76^th place

1psu.edu

207^th place

136^th place

doi.org

Levinthal C, Wodak SJ, Kahn P, Dadivanian AK (1975). "Hemoglobin Interactions in Sickle Cell Fibers: I. Theoretical Approaches to the Molecular Contacts". Proceedings of the National Academy of Sciences. 72 (4): 1330–1334. Bibcode:1975PNAS...72.1330L. doi:10.1073/pnas.72.4.1330. PMC 432527. PMID 1055409.
Wodak SJ, Janin J (1978). "Computer Analysis of Protein-Protein Interactions". Journal of Molecular Biology. 124 (2): 323–342. doi:10.1016/0022-2836(78)90302-9. PMID 712840.
Wodak SJ, De Crombrugghe M, Janin J (1987). "Computer Studies of Interactions between Macromolecules". Progress in Biophysics and Molecular Biology. 49 (1): 29–63. doi:10.1016/0079-6107(87)90008-3. PMID 3310103.
Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA (1992). "Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques". Proc. Natl. Acad. Sci. U.S.A. 89 (6): 2195–2199. Bibcode:1992PNAS...89.2195K. doi:10.1073/pnas.89.6.2195. PMC 48623. PMID 1549581.
Gabb HA, Jackson RM, Sternberg MJ (September 1997). "Modelling protein docking using shape complementarity, electrostatics and biochemical information". J. Mol. Biol. 272 (1): 106–120. doi:10.1006/jmbi.1997.1203. PMID 9299341.
Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN (1996). "Molecular Docking Programs Successfully Predict the Binding of a Beta-lactamase Inhibitory Protein to TEM-1 Beta-Lactamase". Nature Structural & Molecular Biology. 3 (3): 233–239. doi:10.1038/nsb0396-233. PMID 8605624. S2CID 40212654.
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D (2003). "Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations". J. Mol. Biol. 331 (1): 281–299. doi:10.1016/S0022-2836(03)00670-3. PMID 12875852.
Camacho CJ, Vajda S (2008). "Protein docking along smooth association pathways". Proceedings of the National Academy of Sciences. 98 (19): 10636–10641. doi:10.1073/pnas.181147798. PMC 58518. PMID 11517309.
Camacho CJ, Vajda S (2007). "In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach". BMC Structural Biology. 7: 37. doi:10.1186/1472-6807-7-37. PMC 1913526. PMID 17559675.
Zhang C, Liu S, Zhu Q, Zhou Y (2005). "A knowledge-based energy function for protein–ligand, protein–protein, and protein–DNA complexes". Journal of Medicinal Chemistry. 48 (7): 2325–2335. doi:10.1021/jm049314d. PMID 15801826.
Esmaielbeiki R, Nebel JC (2014). "Scoring docking conformations using predicted protein interfaces". BMC Bioinformatics. 15: 171. doi:10.1186/1471-2105-15-171. PMC 4057934. PMID 24906633.
Kastritis PL, Bonvin AM (May 2010). "Are scoring functions in protein–protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark". J. Proteome Res. 9 (5): 2216–2225. doi:10.1021/pr9009854. hdl:1874/202590. PMID 20329755.
Badal, VD, Kundrotas, PJ, Vakser, IA (2018). "Natural language processing in text mining for structural modeling of protein complexes". BMC Bioinformatics. 19 (1): 84. doi:10.1186/s12859-018-2079-4. PMC 5838950. PMID 29506465.
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). "Protein-Protein Docking Benchmark 2.0: an update". Proteins. 60 (2): 214–216. doi:10.1002/prot.20560. PMID 15981264. S2CID 24049376.
Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z (September 2015). "Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2". Journal of Molecular Biology. 427 (19): 3031–41. doi:10.1016/j.jmb.2015.07.016. PMC 4677049. PMID 26231283.
van Dijk M, Bonvin AM (August 2008). "A protein-DNA docking benchmark". Nucleic Acids Research. 36 (14): e88. doi:10.1093/nar/gkn386. PMC 2504314. PMID 18583363.
Barik A, C N, P M, Bahadur RP (July 2012). "A protein-RNA docking benchmark (I): nonredundant cases". Proteins. 80 (7): 1866–71. doi:10.1002/prot.24083. PMID 22488669. S2CID 437472.
Pérez-Cano L, Jiménez-García B, Fernández-Recio J (July 2012). "A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data". Proteins. 80 (7): 1872–82. doi:10.1002/prot.24075. PMID 22488990. S2CID 20322388.
Nithin C, Mukherjee S, Bahadur RP (November 2016). "A non-redundant protein-RNA docking benchmark version 2.0". Proteins. 85 (2): 256–267. doi:10.1002/prot.25211. PMID 27862282. S2CID 26814049.
Nithin, Chandran; Ghosh, Pritha; Bujnicki, Janusz; Nithin, Chandran; Ghosh, Pritha; Bujnicki, Janusz M. (2018-08-25). "Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes". Genes. 9 (9): 432. doi:10.3390/genes9090432. PMC 6162694. PMID 30149645.
Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J (March 2011). "A structure-based benchmark for protein-protein binding affinity". Protein Science. 20 (3): 482–491. doi:10.1002/pro.580. PMC 3064828. PMID 21213247.
Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ (2003). "CAPRI: a Critical Assessment of PRedicted Interactions". Proteins. 52 (1): 2–9. CiteSeerX 10.1.1.461.3355. doi:10.1002/prot.10381. PMID 12784359. S2CID 31489448.

handle.net

hdl.handle.net

Kastritis PL, Bonvin AM (May 2010). "Are scoring functions in protein–protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark". J. Proteome Res. 9 (5): 2216–2225. doi:10.1021/pr9009854. hdl:1874/202590. PMID 20329755.

harvard.edu

ui.adsabs.harvard.edu

Levinthal C, Wodak SJ, Kahn P, Dadivanian AK (1975). "Hemoglobin Interactions in Sickle Cell Fibers: I. Theoretical Approaches to the Molecular Contacts". Proceedings of the National Academy of Sciences. 72 (4): 1330–1334. Bibcode:1975PNAS...72.1330L. doi:10.1073/pnas.72.4.1330. PMC 432527. PMID 1055409.
Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA (1992). "Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques". Proc. Natl. Acad. Sci. U.S.A. 89 (6): 2195–2199. Bibcode:1992PNAS...89.2195K. doi:10.1073/pnas.89.6.2195. PMC 48623. PMID 1549581.

nih.gov

pubmed.ncbi.nlm.nih.gov

Levinthal C, Wodak SJ, Kahn P, Dadivanian AK (1975). "Hemoglobin Interactions in Sickle Cell Fibers: I. Theoretical Approaches to the Molecular Contacts". Proceedings of the National Academy of Sciences. 72 (4): 1330–1334. Bibcode:1975PNAS...72.1330L. doi:10.1073/pnas.72.4.1330. PMC 432527. PMID 1055409.
Wodak SJ, Janin J (1978). "Computer Analysis of Protein-Protein Interactions". Journal of Molecular Biology. 124 (2): 323–342. doi:10.1016/0022-2836(78)90302-9. PMID 712840.
Wodak SJ, De Crombrugghe M, Janin J (1987). "Computer Studies of Interactions between Macromolecules". Progress in Biophysics and Molecular Biology. 49 (1): 29–63. doi:10.1016/0079-6107(87)90008-3. PMID 3310103.
Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA (1992). "Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques". Proc. Natl. Acad. Sci. U.S.A. 89 (6): 2195–2199. Bibcode:1992PNAS...89.2195K. doi:10.1073/pnas.89.6.2195. PMC 48623. PMID 1549581.
Gabb HA, Jackson RM, Sternberg MJ (September 1997). "Modelling protein docking using shape complementarity, electrostatics and biochemical information". J. Mol. Biol. 272 (1): 106–120. doi:10.1006/jmbi.1997.1203. PMID 9299341.
Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN (1996). "Molecular Docking Programs Successfully Predict the Binding of a Beta-lactamase Inhibitory Protein to TEM-1 Beta-Lactamase". Nature Structural & Molecular Biology. 3 (3): 233–239. doi:10.1038/nsb0396-233. PMID 8605624. S2CID 40212654.
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D (2003). "Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations". J. Mol. Biol. 331 (1): 281–299. doi:10.1016/S0022-2836(03)00670-3. PMID 12875852.
Camacho CJ, Vajda S (2008). "Protein docking along smooth association pathways". Proceedings of the National Academy of Sciences. 98 (19): 10636–10641. doi:10.1073/pnas.181147798. PMC 58518. PMID 11517309.
Camacho CJ, Vajda S (2007). "In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach". BMC Structural Biology. 7: 37. doi:10.1186/1472-6807-7-37. PMC 1913526. PMID 17559675.
Zhang C, Liu S, Zhu Q, Zhou Y (2005). "A knowledge-based energy function for protein–ligand, protein–protein, and protein–DNA complexes". Journal of Medicinal Chemistry. 48 (7): 2325–2335. doi:10.1021/jm049314d. PMID 15801826.
Esmaielbeiki R, Nebel JC (2014). "Scoring docking conformations using predicted protein interfaces". BMC Bioinformatics. 15: 171. doi:10.1186/1471-2105-15-171. PMC 4057934. PMID 24906633.
Kastritis PL, Bonvin AM (May 2010). "Are scoring functions in protein–protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark". J. Proteome Res. 9 (5): 2216–2225. doi:10.1021/pr9009854. hdl:1874/202590. PMID 20329755.
Badal, VD, Kundrotas, PJ, Vakser, IA (2018). "Natural language processing in text mining for structural modeling of protein complexes". BMC Bioinformatics. 19 (1): 84. doi:10.1186/s12859-018-2079-4. PMC 5838950. PMID 29506465.
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). "Protein-Protein Docking Benchmark 2.0: an update". Proteins. 60 (2): 214–216. doi:10.1002/prot.20560. PMID 15981264. S2CID 24049376.
Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z (September 2015). "Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2". Journal of Molecular Biology. 427 (19): 3031–41. doi:10.1016/j.jmb.2015.07.016. PMC 4677049. PMID 26231283.
van Dijk M, Bonvin AM (August 2008). "A protein-DNA docking benchmark". Nucleic Acids Research. 36 (14): e88. doi:10.1093/nar/gkn386. PMC 2504314. PMID 18583363.
Barik A, C N, P M, Bahadur RP (July 2012). "A protein-RNA docking benchmark (I): nonredundant cases". Proteins. 80 (7): 1866–71. doi:10.1002/prot.24083. PMID 22488669. S2CID 437472.
Pérez-Cano L, Jiménez-García B, Fernández-Recio J (July 2012). "A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data". Proteins. 80 (7): 1872–82. doi:10.1002/prot.24075. PMID 22488990. S2CID 20322388.
Nithin C, Mukherjee S, Bahadur RP (November 2016). "A non-redundant protein-RNA docking benchmark version 2.0". Proteins. 85 (2): 256–267. doi:10.1002/prot.25211. PMID 27862282. S2CID 26814049.
Nithin, Chandran; Ghosh, Pritha; Bujnicki, Janusz; Nithin, Chandran; Ghosh, Pritha; Bujnicki, Janusz M. (2018-08-25). "Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes". Genes. 9 (9): 432. doi:10.3390/genes9090432. PMC 6162694. PMID 30149645.
Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J (March 2011). "A structure-based benchmark for protein-protein binding affinity". Protein Science. 20 (3): 482–491. doi:10.1002/pro.580. PMC 3064828. PMID 21213247.
Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ (2003). "CAPRI: a Critical Assessment of PRedicted Interactions". Proteins. 52 (1): 2–9. CiteSeerX 10.1.1.461.3355. doi:10.1002/prot.10381. PMID 12784359. S2CID 31489448.

ncbi.nlm.nih.gov

Levinthal C, Wodak SJ, Kahn P, Dadivanian AK (1975). "Hemoglobin Interactions in Sickle Cell Fibers: I. Theoretical Approaches to the Molecular Contacts". Proceedings of the National Academy of Sciences. 72 (4): 1330–1334. Bibcode:1975PNAS...72.1330L. doi:10.1073/pnas.72.4.1330. PMC 432527. PMID 1055409.
Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA (1992). "Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques". Proc. Natl. Acad. Sci. U.S.A. 89 (6): 2195–2199. Bibcode:1992PNAS...89.2195K. doi:10.1073/pnas.89.6.2195. PMC 48623. PMID 1549581.
Camacho CJ, Vajda S (2008). "Protein docking along smooth association pathways". Proceedings of the National Academy of Sciences. 98 (19): 10636–10641. doi:10.1073/pnas.181147798. PMC 58518. PMID 11517309.
Camacho CJ, Vajda S (2007). "In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach". BMC Structural Biology. 7: 37. doi:10.1186/1472-6807-7-37. PMC 1913526. PMID 17559675.
Esmaielbeiki R, Nebel JC (2014). "Scoring docking conformations using predicted protein interfaces". BMC Bioinformatics. 15: 171. doi:10.1186/1471-2105-15-171. PMC 4057934. PMID 24906633.
Badal, VD, Kundrotas, PJ, Vakser, IA (2018). "Natural language processing in text mining for structural modeling of protein complexes". BMC Bioinformatics. 19 (1): 84. doi:10.1186/s12859-018-2079-4. PMC 5838950. PMID 29506465.
Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z (September 2015). "Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2". Journal of Molecular Biology. 427 (19): 3031–41. doi:10.1016/j.jmb.2015.07.016. PMC 4677049. PMID 26231283.
van Dijk M, Bonvin AM (August 2008). "A protein-DNA docking benchmark". Nucleic Acids Research. 36 (14): e88. doi:10.1093/nar/gkn386. PMC 2504314. PMID 18583363.
Nithin, Chandran; Ghosh, Pritha; Bujnicki, Janusz; Nithin, Chandran; Ghosh, Pritha; Bujnicki, Janusz M. (2018-08-25). "Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes". Genes. 9 (9): 432. doi:10.3390/genes9090432. PMC 6162694. PMID 30149645.
Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J (March 2011). "A structure-based benchmark for protein-protein binding affinity". Protein Science. 20 (3): 482–491. doi:10.1002/pro.580. PMC 3064828. PMID 21213247.

psu.edu

citeseerx.ist.psu.edu

Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ (2003). "CAPRI: a Critical Assessment of PRedicted Interactions". Proteins. 52 (1): 2–9. CiteSeerX 10.1.1.461.3355. doi:10.1002/prot.10381. PMID 12784359. S2CID 31489448.

semanticscholar.org

api.semanticscholar.org

Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN (1996). "Molecular Docking Programs Successfully Predict the Binding of a Beta-lactamase Inhibitory Protein to TEM-1 Beta-Lactamase". Nature Structural & Molecular Biology. 3 (3): 233–239. doi:10.1038/nsb0396-233. PMID 8605624. S2CID 40212654.
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). "Protein-Protein Docking Benchmark 2.0: an update". Proteins. 60 (2): 214–216. doi:10.1002/prot.20560. PMID 15981264. S2CID 24049376.
Barik A, C N, P M, Bahadur RP (July 2012). "A protein-RNA docking benchmark (I): nonredundant cases". Proteins. 80 (7): 1866–71. doi:10.1002/prot.24083. PMID 22488669. S2CID 437472.
Pérez-Cano L, Jiménez-García B, Fernández-Recio J (July 2012). "A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data". Proteins. 80 (7): 1872–82. doi:10.1002/prot.24075. PMID 22488990. S2CID 20322388.
Nithin C, Mukherjee S, Bahadur RP (November 2016). "A non-redundant protein-RNA docking benchmark version 2.0". Proteins. 85 (2): 256–267. doi:10.1002/prot.25211. PMID 27862282. S2CID 26814049.
Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ (2003). "CAPRI: a Critical Assessment of PRedicted Interactions". Proteins. 52 (1): 2–9. CiteSeerX 10.1.1.461.3355. doi:10.1002/prot.10381. PMID 12784359. S2CID 31489448.