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Items: 1 to 20 of 85

1.

Use of fast conformational sampling to improve the characterization of VEGF A-peptide interactions.

Wu G, Han K, Lv F.

J Theor Biol. 2013 Jan 21;317:293-300. doi: 10.1016/j.jtbi.2012.10.021.

PMID:
23098896
2.

Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain.

Hou T, Zhang W, Case DA, Wang W.

J Mol Biol. 2008 Feb 29;376(4):1201-14. doi: 10.1016/j.jmb.2007.12.054.

PMID:
18206907
3.

Solution structure of a phage-derived peptide antagonist in complex with vascular endothelial growth factor.

Pan B, Li B, Russell SJ, Tom JY, Cochran AG, Fairbrother WJ.

J Mol Biol. 2002 Feb 22;316(3):769-87.

PMID:
11866530
4.

Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK.

Kasper P, Christen P, Gehring H.

Proteins. 2000 Aug 1;40(2):185-92.

PMID:
10842335
5.

Fast and reliable prediction of domain-peptide binding affinity using coarse-grained structure models.

Tian F, Tan R, Guo T, Zhou P, Yang L.

Biosystems. 2013 Jul;113(1):40-9. doi: 10.1016/j.biosystems.2013.04.004.

PMID:
23665477
6.

Molecular docking and analysis of interactions between vascular endothelial growth factor (VEGF) and SPARC protein.

Chandrasekaran V, Ambati J, Ambati BK, Taylor EW.

J Mol Graph Model. 2007 Nov;26(4):775-82.

PMID:
17560152
7.

Modulation, bioinformatic screening, and assessment of small molecular peptides targeting the vascular endothelial growth factor receptor.

Feng S, Zou L, Ni Q, Zhang X, Li Q, Zheng L, Xie L, Li H, Huang D.

Cell Biochem Biophys. 2014 Dec;70(3):1913-21. doi: 10.1007/s12013-014-0151-x.

8.

On the structure, interactions, and dynamics of bound VEGF.

Horta BA, Cirino JJ, de Alencastro RB.

J Mol Graph Model. 2008 Apr;26(7):1091-103.

PMID:
18023381
9.

Crystal structure of the complex between VEGF and a receptor-blocking peptide.

Wiesmann C, Christinger HW, Cochran AG, Cunningham BC, Fairbrother WJ, Keenan CJ, Meng G, de Vos AM.

Biochemistry. 1998 Dec 22;37(51):17765-72.

PMID:
9922142
10.
11.

Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses.

Tian F, Lv Y, Zhou P, Yang L.

J Comput Aided Mol Des. 2011 Oct;25(10):947-58. doi: 10.1007/s10822-011-9474-5.

PMID:
21964565
12.

Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential.

Liu Z, Dominy BN, Shakhnovich EI.

J Am Chem Soc. 2004 Jul 14;126(27):8515-28.

PMID:
15238009
13.

Thermodynamic additivity of sequence variations: an algorithm for creating high affinity peptides without large libraries or structural information.

Greving MP, Belcher PE, Diehnelt CW, Gonzalez-Moa MJ, Emery J, Fu J, Johnston SA, Woodbury NW.

PLoS One. 2010 Nov 11;5(11):e15432. doi: 10.1371/journal.pone.0015432.

14.

Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses.

Tian F, Yang L, Lv F, Luo X, Pan Y.

Amino Acids. 2011 Feb;40(2):493-503. doi: 10.1007/s00726-010-0661-9.

PMID:
20582607
15.
16.

Targeting diverse protein-protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold.

Checco JW, Kreitler DF, Thomas NC, Belair DG, Rettko NJ, Murphy WL, Forest KT, Gellman SH.

Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4552-7. doi: 10.1073/pnas.1420380112.

17.

Analysis of the thermodynamics of binding of an SH3 domain to proline-rich peptides using a chimeric fusion protein.

Candel AM, van Nuland NA, Martin-Sierra FM, Martinez JC, Conejero-Lara F.

J Mol Biol. 2008 Mar 14;377(1):117-35. doi: 10.1016/j.jmb.2007.11.060.

PMID:
18234212
18.

Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein.

Zuo Z, Gandhi NS, Arndt KM, Mancera RL.

Biopolymers. 2012 Nov;97(11):899-909. doi: 10.1002/bip.22099.

PMID:
22899365
20.

Helical peptides from VEGF and Vammin hotspots for modulating the VEGF-VEGFR interaction.

García-Aranda MI, González-López S, Santiveri CM, Gagey-Eilstein N, Reille-Seroussi M, Martín-Martínez M, Inguimbert N, Vidal M, García-López MT, Jiménez MA, González-Muñiz R, Pérez de Vega MJ.

Org Biomol Chem. 2013 Mar 21;11(11):1896-905. doi: 10.1039/c3ob27312a.

PMID:
23381088
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