Molecular simulation methods for selecting thrombin-binding aptamers

Lecture Notes in Electrical Engineering

Volumn 253 LNEE, Issue , 2013, Pages 743-749

  Kumar, Jangam Vikram ^a   Chen, Wen Yih ^b   Tsai, Jeffrey J P ^a   Hu, Wen Pin ^a  

^a ASIA UNIVERSITY   (Taiwan)

^b NATIONAL CENTRAL UNIVERSITY   (Taiwan)

Author keywords

Aptamers; Molecular simulation; Pairwise shape complementarity; Selection; Thrombin

Indexed keywords

BINDING ENERGY; COMPUTER SOFTWARE; MOLECULAR STRUCTURE; ROBOTICS; TELECOMMUNICATION SERVICES;

APTAMERS; MOLECULAR SIMULATIONS; SELECTION; SHAPE COMPLEMENTARITY; THROMBIN;

ENZYMES;

EID: 84881183786     PISSN: 18761100     EISSN: 18761119     Source Type: Book Series    
DOI: 10.1007/978-94-007-6996-0_78     Document Type: Conference Paper

References (11)

1. Brown CJ, Dastidar SG, See HY, Coomber DW, Ortiz-Lombardia M, Verma C, Lane DP (2010) Rational design and biophysical characterization of thioredoxin-based aptamers: insights into peptide grafting. J Mol Biol 395:871-883
2. Gabb HA, Jackson RM, Sternberg MJE (1997) Modeling protein docking using shape complementarity, electrostatics and biochemical information. J Molec Bio 272:106-120
3. Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, Tsigelny I, Ten Eyck LF (2001) Protein docking using continuum electrostatics and geometric fit. Prot Eng 14:105-113
4. Vakser IA (1997) Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins. Sl:226-230
5. Chen R, Mintseris J, Janin J, Weng Z (2003) A protein-protein docking benchmark. Proteins 52:88-91
6. Pierce B, Weng Z (2008) A combination of rescoring and refinement significantly improves protein docking performance. Proteins 72:270-279
7. Chen R, Weng Z (2003) ZDOCK: an Initial-stage protein-docking algorithm. Proteins 52:80-87
8. Chen R, Weng Z (2003) A novel shape complementarity scoring function for protein-protein docking. Proteins 51:397-408
9. Vajda S, Camacho CJ (2004) Protein-protein docking: is the glass half-full or half-empty? Trends Biotech 22:110-116
10. Macaya RF, Schultze P, Smith FW, Roe JA, Feigon J (1993) Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. Proc Natl Acad Sci USA 90:3745-3749
11. Bini A, Mascini M, Mascini M, Turner AP (2011) Selection of thrombin-binding aptamers by using computational approach for aptasensor application. Biosens Bioelectron 26:4411-4416