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Items: 1 to 20 of 101

1.

Comprehensive in silico mutagenesis highlights functionally important residues in proteins.

Bromberg Y, Rost B.

Bioinformatics. 2008 Aug 15;24(16):i207-12. doi: 10.1093/bioinformatics/btn268.

2.

A two-stage classifier for identification of protein-protein interface residues.

Yan C, Dobbs D, Honavar V.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i371-8.

PMID:
15262822
3.

Prediction of hot spots in protein interfaces using a random forest model with hybrid features.

Wang L, Liu ZP, Zhang XS, Chen L.

Protein Eng Des Sel. 2012 Mar;25(3):119-26. doi: 10.1093/protein/gzr066. Epub 2012 Jan 18.

PMID:
22258275
4.

Construction and application of the weighted amino acid network based on energy.

Jiao X, Chang S, Li CH, Chen WZ, Wang CX.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 May;75(5 Pt 1):051903. Epub 2007 May 4.

PMID:
17677094
5.

ISIS: interaction sites identified from sequence.

Ofran Y, Rost B.

Bioinformatics. 2007 Jan 15;23(2):e13-6.

PMID:
17237081
6.

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy.

Tuncbag N, Gursoy A, Keskin O.

Bioinformatics. 2009 Jun 15;25(12):1513-20. doi: 10.1093/bioinformatics/btp240. Epub 2009 Apr 8.

PMID:
19357097
7.

Protein-protein interaction hotspots carved into sequences.

Ofran Y, Rost B.

PLoS Comput Biol. 2007 Jul;3(7):e119.

8.

Stochastic roadmap simulation for the study of ligand-protein interactions.

Apaydin MS, Guestrin CE, Varma C, Brutlag DL, Latombe JC.

Bioinformatics. 2002;18 Suppl 2:S18-26.

PMID:
12385979
9.

On the asymmetry of the residue compositions of the binding sites on protein surfaces.

Iván G, Szabadka Z, Grolmusz V.

J Bioinform Comput Biol. 2009 Dec;7(6):931-8.

PMID:
20014471
10.

Prediction of DNA-binding residues from sequence.

Ofran Y, Mysore V, Rost B.

Bioinformatics. 2007 Jul 1;23(13):i347-53.

PMID:
17646316
11.

Prediction of Ras-effector interactions using position energy matrices.

Kiel C, Serrano L.

Bioinformatics. 2007 Sep 1;23(17):2226-30. Epub 2007 Jun 28.

PMID:
17599936
12.

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.

Laurie AT, Jackson RM.

Bioinformatics. 2005 May 1;21(9):1908-16. Epub 2005 Feb 8.

PMID:
15701681
13.

Intramolecular surface contacts contain information about protein-protein interface regions.

de Vries SJ, Bonvin AM.

Bioinformatics. 2006 Sep 1;22(17):2094-8. Epub 2006 Jun 9.

PMID:
16766554
14.

Properties of contact matrices induced by pairwise interactions in proteins.

Miyazawa S, Kinjo AR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 May;77(5 Pt 1):051910. Epub 2008 May 14.

PMID:
18643105
15.

FastContact: rapid estimate of contact and binding free energies.

Camacho CJ, Zhang C.

Bioinformatics. 2005 May 15;21(10):2534-6. Epub 2005 Feb 15.

PMID:
15713734
16.

Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets.

Launay G, Mendez R, Wodak S, Simonson T.

BMC Bioinformatics. 2007 Jul 27;8:270.

17.

Prediction of hot spots in protein interfaces using extreme learning machines with the information of spatial neighbour residues.

Wang L, Zhang W, Gao Q, Xiong C.

IET Syst Biol. 2014 Aug;8(4):184-90. doi: 10.1049/iet-syb.2013.0049.

PMID:
25075532
18.

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.

Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A.

PLoS Comput Biol. 2009 Jan;5(1):e1000267. doi: 10.1371/journal.pcbi.1000267. Epub 2009 Jan 23.

19.

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
20.

The role of site-directed point mutations in protein misfolding.

Baruah A, Biswas P.

Phys Chem Chem Phys. 2014 Jul 21;16(27):13964-73. doi: 10.1039/c3cp55367a. Epub 2014 Jun 5.

PMID:
24898496

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