Understanding the molecular mechanism of the broad and potent neutralization of HIV-1 by antibody VRC01 from the perspective of molecular dynamics simulation and binding free energy calculations

Journal of Molecular Modeling

Volumn 18, Issue 9, 2012, Pages 4517-4527

  Zhang, Yan ^a   Pan, Dabo ^a   Shen, Yulin ^c   Jin, Nengzhi ^c   Liu, Huanxiang ^a,b   Yao, Xiaojun ^b  

^a LANZHOU UNIVERSITY   (China)

^b LANZHOU UNIVERSITY   (China)

^c Gansu Computing Center   (China)

Author keywords

Gp120; HIV 1; MM GBSA; MM PBSA; Molecular dynamics simulation; VRC01

Indexed keywords

ARGININE; GLYCINE; GLYCOPROTEIN GP 120; HUMAN IMMUNODEFICIENCY VIRUS ANTIBODY; HUMAN IMMUNODEFICIENCY VIRUS ANTIBODY VRC01; LYSINE; NEUTRALIZING ANTIBODY; TRYPSIN; UNCLASSIFIED DRUG;

AMINO ACID ANALYSIS; ANTIGEN BINDING; ARTICLE; BINDING KINETICS; CHEMICAL INTERACTION; CLADISTICS; CLUSTER ANALYSIS; CRYSTAL STRUCTURE; DECOMPOSITION; HEAVY CHAIN; HUMAN IMMUNODEFICIENCY VIRUS 1; LIGHT CHAIN; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; SIMULATION; STRUCTURE ANALYSIS; VIRUS NEUTRALIZATION;

AMINO ACIDS; ANTIBODIES, NEUTRALIZING; CLUSTER ANALYSIS; HIV ANTIBODIES; HIV ENVELOPE PROTEIN GP120; HIV-1; HUMANS; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; PRINCIPAL COMPONENT ANALYSIS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS; TIME FACTORS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84867580370     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-012-1450-z     Document Type: Article

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