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Items: 1 to 20 of 100

1.

Probabilistic prediction of contacts in protein-ligand complexes.

Hakulinen R, Puranen S, Lehtonen JV, Johnson MS, Corander J.

PLoS One. 2012;7(11):e49216. doi: 10.1371/journal.pone.0049216. Epub 2012 Nov 14.

2.

Binding affinity prediction for protein-ligand complexes based on β contacts and B factor.

Liu Q, Kwoh CK, Li J.

J Chem Inf Model. 2013 Nov 25;53(11):3076-85. doi: 10.1021/ci400450h. Epub 2013 Nov 5.

PMID:
24191692
3.

GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes.

Kasahara K, Kinoshita K.

BMC Bioinformatics. 2014 Jan 14;15:12. doi: 10.1186/1471-2105-15-12.

4.

Statistical potential for modeling and ranking of protein-ligand interactions.

Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A.

J Chem Inf Model. 2011 Dec 27;51(12):3078-92. doi: 10.1021/ci200377u. Epub 2011 Nov 21.

5.

Information theory-based scoring function for the structure-based prediction of protein-ligand binding affinity.

Kulharia M, Goody RS, Jackson RM.

J Chem Inf Model. 2008 Oct;48(10):1990-8. doi: 10.1021/ci800125k. Epub 2008 Sep 4.

PMID:
18767831
6.
7.
8.

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.

Ravindranath PA, Forli S, Goodsell DS, Olson AJ, Sanner MF.

PLoS Comput Biol. 2015 Dec 2;11(12):e1004586. doi: 10.1371/journal.pcbi.1004586. eCollection 2015 Dec.

9.

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.

Najmanovich R, Kurbatova N, Thornton J.

Bioinformatics. 2008 Aug 15;24(16):i105-11. doi: 10.1093/bioinformatics/btn263.

10.

Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions.

Kasahara K, Shirota M, Kinoshita K.

J Chem Inf Model. 2013 Jan 28;53(1):241-8. doi: 10.1021/ci300377f. Epub 2012 Dec 18.

PMID:
23186137
11.
13.

Knowledge-based scoring function to predict protein-ligand interactions.

Gohlke H, Hendlich M, Klebe G.

J Mol Biol. 2000 Jan 14;295(2):337-56.

PMID:
10623530
14.

Parameter estimation for scoring protein-ligand interactions using negative training data.

Pham TA, Jain AN.

J Med Chem. 2006 Oct 5;49(20):5856-68.

PMID:
17004701
15.

Are predefined decoy sets of ligand poses able to quantify scoring function accuracy?

Korb O, Ten Brink T, Victor Paul Raj FR, Keil M, Exner TE.

J Comput Aided Mol Des. 2012 Feb;26(2):185-97. doi: 10.1007/s10822-011-9539-5. Epub 2012 Jan 10.

PMID:
22231069
16.

A novel ligand-mapping method based on molecular liquid theory.

Imai T.

Curr Pharm Des. 2011;17(17):1685-94.

PMID:
21619527
17.

Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations.

Raman EP, Yu W, Guvench O, Mackerell AD.

J Chem Inf Model. 2011 Apr 25;51(4):877-96. doi: 10.1021/ci100462t. Epub 2011 Apr 1.

18.

Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions.

Søndergaard CR, Garrett AE, Carstensen T, Pollastri G, Nielsen JE.

J Med Chem. 2009 Sep 24;52(18):5673-84. doi: 10.1021/jm8016464.

PMID:
19711919
19.

Investigation of atomic level patterns in protein--small ligand interactions.

Chen K, Kurgan L.

PLoS One. 2009;4(2):e4473. doi: 10.1371/journal.pone.0004473. Epub 2009 Feb 16.

20.

A scoring function for docking ligands to low-resolution protein structures.

Bindewald E, Skolnick J.

J Comput Chem. 2005 Mar;26(4):374-83.

PMID:
15651033

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