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Similar articles for PubMed (Select 23217202)

1.

Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling.

Smith N, Campbell B, Li L, Li C, Alexov E.

BMC Struct Biol. 2012 Dec 5;12:31. doi: 10.1186/1472-6807-12-31.

2.

DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol.

Smith N, Witham S, Sarkar S, Zhang J, Li L, Li C, Alexov E.

Bioinformatics. 2012 Jun 15;28(12):1655-7. doi: 10.1093/bioinformatics/bts200. Epub 2012 Apr 23.

3.

H++: a server for estimating pKas and adding missing hydrogens to macromolecules.

Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W368-71.

4.

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations.

Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W665-7.

5.
6.

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

Kinoshita K, Murakami Y, Nakamura H.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W398-402. Epub 2007 Jun 12.

7.
8.

PDB Goodies--a web-based GUI to manipulate the Protein Data Bank file.

Hussain AS, Shanthi V, Sheik SS, Jeyakanthan J, Selvarani P, Sekar K.

Acta Crystallogr D Biol Crystallogr. 2002 Aug;58(Pt 8):1385-6. Epub 2002 Jul 20.

PMID:
12136164
9.

BALLView: an object-oriented molecular visualization and modeling framework.

Moll A, Hildebrandt A, Lenhof HP, Kohlbacher O.

J Comput Aided Mol Des. 2005 Nov;19(11):791-800. Epub 2006 Feb 10.

PMID:
16470421
10.

PreBI: prediction of biological interfaces of proteins in crystals.

Tsuchiya Y, Kinoshita K, Ito N, Nakamura H.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W320-4.

11.

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations.

Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W522-5. Epub 2007 May 8.

12.

ProBLM web server: protein and membrane placement and orientation package.

Kimmett T, Smith N, Witham S, Petukh M, Sarkar S, Alexov E.

Comput Math Methods Med. 2014;2014:838259. doi: 10.1155/2014/838259. Epub 2014 Jul 14.

13.

Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii.

Fogolari F, Corazza A, Yarra V, Jalaru A, Viglino P, Esposito G.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S18. doi: 10.1186/1471-2105-13-S4-S18.

14.

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.

15.

GROMACS molecule & liquid database.

van der Spoel D, van Maaren PJ, Caleman C.

Bioinformatics. 2012 Mar 1;28(5):752-3. doi: 10.1093/bioinformatics/bts020. Epub 2012 Jan 11.

16.

Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces.

Shazman S, Celniker G, Haber O, Glaser F, Mandel-Gutfreund Y.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W526-30. Epub 2007 May 30.

17.

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

Azuara C, Lindahl E, Koehl P, Orland H, Delarue M.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W38-42.

18.

DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes.

Sarkar S, Witham S, Zhang J, Zhenirovskyy M, Rocchia W, Alexov E.

Commun Comput Phys. 2013 Jan;13(1):269-284.

19.

WEBnm@: a web application for normal mode analyses of proteins.

Hollup SM, Salensminde G, Reuter N.

BMC Bioinformatics. 2005 Mar 11;6:52.

20.

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

Wang L, Rodriguez-Tomé P, Redaschi N, McNeil P, Robinson A, Lijnzaad P.

Genome Biol. 2000;1(5):RESEARCH0010. Epub 2000 Nov 6.

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