Biomaterial Database

Efficient estimation of MMGBSA-based BEs for DNA and aromatic furan amidino derivatives. 2013

Hemant Kumar Srivastava, and G Narahari Sastry

Molecular Modelling Group, Indian Institute of Chemical Technology, Uppal Road, Taranaka, Hyderabad 500 607, India. hemantkrsri@gmail.com

Molecular mechanics with Generalized Born surface area (MMGBSA) based binding energies (BEs) derived from the molecular dynamics (MD) trajectories are highly reliable and extensively used standards to estimate the strength of interactions between ligands and their receptor. MD simulations (5 ns) for 30 aromatic furan aminidino derivatives (anti-Pneumocystis carnii agents) have been carried out by using Amber program and BEs have been calculated by using Generalized Born (GB) method. Based on the generated data, we present a simple and effective method for the approximation of BEs without performing MD simulations and MMGBSA calculations. Quantum chemical (density functional theory based) and geometrical descriptors are used for the prediction of the BE values. All the developed models are statistically significant with high values of correlation and cross-validation coefficients. The prediction ability and effectiveness of the models are tested by the division of the data-set into four different training and test sets and the average error was only 4-7% (1.56-2.61 kcal/mol) of the actual BEs.

UI	MeSH Term	Description	Entries
D008024	Ligands	A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)	Ligand
D009690	Nucleic Acid Conformation	The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.	DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D004247	DNA	A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).	DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D005663	Furans	Compounds with a 5-membered ring of four carbons and an oxygen. They are aromatic heterocycles. The reduced form is tetrahydrofuran.	Tetrahydrofurans
D006860	Hydrogen Bonding	A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.	Hydrogen Bonds,Bond, Hydrogen,Hydrogen Bond
D000465	Algorithms	A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.	Algorithm
D000578	Amidines	Derivatives of oxoacids RnE(
D044366	Transition Temperature	The temperature at which a substance changes from one state or conformation of matter to another.	Temperature, Transition,Boiling Point Temperature,Freezing Point Temperature,Melting Point Temperature,Boiling Point Temperatures,Freezing Point Temperatures,Melting Point Temperatures,Temperature, Boiling Point,Temperature, Freezing Point,Temperature, Melting Point,Temperatures, Boiling Point,Temperatures, Freezing Point,Temperatures, Melting Point,Temperatures, Transition,Transition Temperatures
D056004	Molecular Dynamics Simulation	A computer simulation developed to study the motion of molecules over a period of time.	Molecular Dynamics Simulations,Molecular Dynamics,Dynamic, Molecular,Dynamics Simulation, Molecular,Dynamics Simulations, Molecular,Dynamics, Molecular,Molecular Dynamic,Simulation, Molecular Dynamics,Simulations, Molecular Dynamics
D021281	Quantitative Structure-Activity Relationship	A quantitative prediction of the biological, ecotoxicological or pharmaceutical activity of a molecule. It is based upon structure and activity information gathered from a series of similar compounds.	Structure Activity Relationship, Quantitative,3D-QSAR,QSAR,QSPR Modeling,Quantitative Structure Property Relationship,3D QSAR,3D-QSARs,Modeling, QSPR,Quantitative Structure Activity Relationship,Quantitative Structure-Activity Relationships,Relationship, Quantitative Structure-Activity,Relationships, Quantitative Structure-Activity,Structure-Activity Relationship, Quantitative,Structure-Activity Relationships, Quantitative