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Items: 1 to 20 of 134

1.

Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residues.

Carl N, Hodošček M, Vehar B, Konc J, Brooks BR, Janežič D.

J Chem Inf Model. 2012 Oct 22;52(10):2541-9. doi: 10.1021/ci3003254. Epub 2012 Oct 8.

2.

Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods.

Lise S, Archambeau C, Pontil M, Jones DT.

BMC Bioinformatics. 2009 Oct 30;10:365. doi: 10.1186/1471-2105-10-365.

3.

ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment.

Konc J, Janezic D.

Bioinformatics. 2010 May 1;26(9):1160-8. doi: 10.1093/bioinformatics/btq100. Epub 2010 Mar 19.

4.

FastContact: a free energy scoring tool for protein-protein complex structures.

Champ PC, Camacho CJ.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W556-60. Epub 2007 May 30.

5.

Small-world network approach to identify key residues in protein-protein interaction.

del Sol A, O'Meara P.

Proteins. 2005 Feb 15;58(3):672-82.

PMID:
15617065
6.

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.

Konc J, Miller BT, Štular T, Lešnik S, Woodcock HL, Brooks BR, Janežič D.

J Chem Inf Model. 2015 Nov 23;55(11):2308-14. doi: 10.1021/acs.jcim.5b00534. Epub 2015 Nov 9.

PMID:
26509288
7.

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility.

Xia JF, Zhao XM, Song J, Huang DS.

BMC Bioinformatics. 2010 Apr 8;11:174. doi: 10.1186/1471-2105-11-174.

8.

Structure-based method for analyzing protein-protein interfaces.

Gao Y, Wang R, Lai L.

J Mol Model. 2004 Feb;10(1):44-54. Epub 2003 Nov 22.

9.

Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes.

Guharoy M, Chakrabarti P.

J Comput Aided Mol Des. 2009 Sep;23(9):645-54. doi: 10.1007/s10822-009-9282-3. Epub 2009 May 29.

PMID:
19479323
10.

DBAC: a simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts.

Li Z, Wong L, Li J.

BMC Syst Biol. 2011 Jun 20;5 Suppl 1:S5. doi: 10.1186/1752-0509-5-S1-S5.

11.

Co-Occurring Atomic Contacts for the Characterization of Protein Binding Hot Spots.

Liu Q, Ren J, Song J, Li J.

PLoS One. 2015 Dec 16;10(12):e0144486. doi: 10.1371/journal.pone.0144486. eCollection 2015.

13.

ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.

Konc J, Cesnik T, Konc JT, Penca M, Janežič D.

J Chem Inf Model. 2012 Feb 27;52(2):604-12. doi: 10.1021/ci2005687. Epub 2012 Feb 7.

14.

Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations.

Liang S, Li L, Hsu WL, Pilcher MN, Uversky V, Zhou Y, Dunker AK, Meroueh SO.

Biochemistry. 2009 Jan 20;48(2):399-414. doi: 10.1021/bi8017043.

15.

Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.

Keskin O, Ma B, Nussinov R.

J Mol Biol. 2005 Feb 4;345(5):1281-94. Epub 2004 Dec 2.

PMID:
15644221
16.

Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes.

Beard H, Cholleti A, Pearlman D, Sherman W, Loving KA.

PLoS One. 2013 Dec 10;8(12):e82849. doi: 10.1371/journal.pone.0082849. eCollection 2013.

17.

Geometrically centered region: a "wet" model of protein binding hot spots not excluding water molecules.

Li Z, Li J.

Proteins. 2010 Dec;78(16):3304-16. doi: 10.1002/prot.22838.

PMID:
20818601
18.

Computational alanine scanning mutagenesis--an improved methodological approach.

Moreira IS, Fernandes PA, Ramos MJ.

J Comput Chem. 2007 Feb;28(3):644-54.

PMID:
17195156
19.

A binding free energy hot spot in the ankyrin repeat protein GABPbeta mediated protein-protein interaction.

Desrosiers DC, Peng ZY.

J Mol Biol. 2005 Nov 25;354(2):375-84. Epub 2005 Oct 3.

PMID:
16243355
20.

Constraining binding hot spots: NMR and molecular dynamics simulations provide a structural explanation for enthalpy-entropy compensation in SH2-ligand binding.

Ward JM, Gorenstein NM, Tian J, Martin SF, Post CB.

J Am Chem Soc. 2010 Aug 18;132(32):11058-70. doi: 10.1021/ja910535j.

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