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Results: 1 to 20 of 102

1.

Data-driven models for protein interaction and design.

Zhu X, Ericksen SS, Demerdash ON, Mitchell JC.

Proteins. 2013 Dec;81(12):2221-8. doi: 10.1002/prot.24405. Epub 2013 Oct 17.

PMID:
24038640
[PubMed - indexed for MEDLINE]
2.

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27.

Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ.

Proteins. 2013 Dec;81(12):2201-9. doi: 10.1002/prot.24425. Epub 2013 Oct 17.

PMID:
24123494
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI).

Huang SY, Yan C, Grinter SZ, Chang S, Jiang L, Zou X.

Proteins. 2013 Dec;81(12):2183-91. doi: 10.1002/prot.24435. Epub 2013 Nov 14.

PMID:
24227686
[PubMed - indexed for MEDLINE]
4.

Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges.

Pallara C, Jiménez-García B, Pérez-Cano L, Romero-Durana M, Solernou A, Grosdidier S, Pons C, Moal IH, Fernandez-Recio J.

Proteins. 2013 Dec;81(12):2192-200. doi: 10.1002/prot.24387. Epub 2013 Oct 17.

PMID:
23934865
[PubMed - indexed for MEDLINE]
5.

Docking, scoring, and affinity prediction in CAPRI.

Lensink MF, Wodak SJ.

Proteins. 2013 Dec;81(12):2082-95. doi: 10.1002/prot.24428. Epub 2013 Oct 17.

PMID:
24115211
[PubMed - indexed for MEDLINE]
6.

Blind predictions of protein interfaces by docking calculations in CAPRI.

Lensink MF, Wodak SJ.

Proteins. 2010 Nov 15;78(15):3085-95. doi: 10.1002/prot.22850.

PMID:
20839234
[PubMed - indexed for MEDLINE]
7.

Flexible docking and refinement with a coarse-grained protein model using ATTRACT.

de Vries S, Zacharias M.

Proteins. 2013 Dec;81(12):2167-74. doi: 10.1002/prot.24400. Epub 2013 Oct 17.

PMID:
23996217
[PubMed - indexed for MEDLINE]
8.

The targets of CAPRI rounds 20-27.

Janin J.

Proteins. 2013 Dec;81(12):2075-81. doi: 10.1002/prot.24375.

PMID:
23900782
[PubMed - indexed for MEDLINE]
9.

Assessing predictions of protein-protein interaction: the CAPRI experiment.

Janin J.

Protein Sci. 2005 Feb;14(2):278-83.

PMID:
15659362
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond.

Qin S, Zhou HX.

Proteins. 2013 Dec;81(12):2229-36. doi: 10.1002/prot.24366. Epub 2013 Sep 14.

PMID:
23873496
[PubMed - indexed for MEDLINE]
11.

Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.

de Vries SJ, Melquiond AS, Kastritis PL, Karaca E, Bordogna A, van Dijk M, Rodrigues JP, Bonvin AM.

Proteins. 2010 Nov 15;78(15):3242-9. doi: 10.1002/prot.22814.

PMID:
20718048
[PubMed - indexed for MEDLINE]
12.

Towards ligand docking including explicit interface water molecules.

Lemmon G, Meiler J.

PLoS One. 2013 Jun 28;8(6):e67536. doi: 10.1371/journal.pone.0067536. Print 2013.

PMID:
23840735
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Improving CAPRI predictions: optimized desolvation for rigid-body docking.

Fernández-Recio J, Abagyan R, Totrov M.

Proteins. 2005 Aug 1;60(2):308-13.

PMID:
15981266
[PubMed - indexed for MEDLINE]
14.

FlexE: efficient molecular docking considering protein structure variations.

Claussen H, Buning C, Rarey M, Lengauer T.

J Mol Biol. 2001 Apr 27;308(2):377-95.

PMID:
11327774
[PubMed - indexed for MEDLINE]
15.

Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models.

Vangone A, Cavallo L, Oliva R.

Proteins. 2013 Dec;81(12):2210-20. doi: 10.1002/prot.24423. Epub 2013 Oct 17.

PMID:
24115176
[PubMed - indexed for MEDLINE]
16.

Assessment of blind predictions of protein-protein interactions: current status of docking methods.

Méndez R, Leplae R, De Maria L, Wodak SJ.

Proteins. 2003 Jul 1;52(1):51-67.

PMID:
12784368
[PubMed - indexed for MEDLINE]
17.

A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces.

Jiang L, Kuhlman B, Kortemme T, Baker D.

Proteins. 2005 Mar 1;58(4):893-904.

PMID:
15651050
[PubMed - indexed for MEDLINE]
18.

On the specificity of heparin/heparan sulfate binding to proteins. Anion-binding sites on antithrombin and thrombin are fundamentally different.

Mosier PD, Krishnasamy C, Kellogg GE, Desai UR.

PLoS One. 2012;7(11):e48632. doi: 10.1371/journal.pone.0048632. Epub 2012 Nov 12.

PMID:
23152789
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Docking and scoring protein complexes: CAPRI 3rd Edition.

Lensink MF, Méndez R, Wodak SJ.

Proteins. 2007 Dec 1;69(4):704-18.

PMID:
17918726
[PubMed - indexed for MEDLINE]
20.

High-resolution protein-protein docking.

Gray JJ.

Curr Opin Struct Biol. 2006 Apr;16(2):183-93. Epub 2006 Mar 20. Review.

PMID:
16546374
[PubMed - indexed for MEDLINE]

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