Journal of Molecular Modeling

Items from 1 to 13 out of 13 results

article

Molecular dynamics simulations of 14 HIV protease mutants in complexes with indinavir

Xianfeng Chen, Irene T. Weber, Robert W. Harrison

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 373-381

The molecular mechanisms of HIV drug resistance were studied using molecular dynamics simulations of HIV-1 protease complexes with the clinical inhibitor indinavir. One nanosecond molecular dynamics simulations were run for solvated complexes of indinavir with wild type protease, a control variant and 12 drug resistant mutants. The quality of the simulations was assessed by comparison with crystallographic...

article

Modeling the E. coli 4-hydroxybenzoic acid oligoprenyltransferase (ubiA transferase) and characterization of potential active sites

Lars Bräuer, Wolfgang Brandt, Ludger A. Wessjohann

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 317-327

4-Hydroxybenzoate oligoprenyltransferase of E. coli, encoded in the gene ubiA, is an important key enzyme in the biosynthetic pathway to ubiquinone. It catalyzes the prenylation of 4-hydroxybenzoic acid in position 3 using an oligoprenyl diphosphate as a second substrate. Up to now, no X-ray structure of this oligoprenyltransferase or any structurally related enzyme is known. Knowledge of the tertiary...

article

Evolutionary trace analysis of ionotropic glutamate receptor sequences and modeling the interactions of agonists with different NMDA receptor subunits

Mathias-Costa Blaise, Ramanathan Sowdhamini, Metpally Raghu Prasad Rao, Nithyananda Pradhan

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 305-316

The ionotropic N-methyl-d-aspartate (NMDA) receptor is of importance in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 or NR3 subunits. We have carried out evolutionary trace (ET) analysis of forty ionotropic glutamate receptor (IGRs) sequences to identify and characterize...

article

Structure and dynamics of Candida rugosa lipase: the role of organic solvent

Bimo Ario Tejo, Abu Bakar Salleh, Juergen Pleiss

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 358-366

The effect of organic solvent on the structure and dynamics of proteins was investigated by multiple molecular dynamics simulations (1 ns each) of Candida rugosa lipase in water and in carbon tetrachloride. The choice of solvent had only a minor structural effect. For both solvents the open and the closed conformation of the lipase were near to their experimental X-ray structures (C_α rms deviation...

article

ProPose: a docking engine based on a fully configurable protein–ligand interaction model

Markus H. J. Seifert, Frank Schmitt, Thomas Herz, Bernd Kramer

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 342-357

Virtual high-throughput screening of molecular databases and in particular high-throughput protein–ligand docking are both common methodologies that identify and enrich hits in the early stages of the drug design process. Current protein–ligand docking algorithms often implement a program-specific model for protein–ligand interaction geometries. However, in order to create a platform for arbitrary...

article

Quantitative structure–activity relationship study on some benzodiazepine derivatives as anti-Alzheimer agents

Bikash Debnath, Shovanlal Gayen, Anindya Basu, Kolluru Srikanth, more

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 328-334

A QSAR study was performed in an attempt to explore the pharmacophore of some benzodiazepine derivatives as anti-Alzheimer agents for the inhibition of γ-secretase. The study, which used the electrotopological state atom (ETSA) index, which encodes electronic and topological information, reveals the importance of two phenyl rings—one substituted and another unsubstituted, for the inhibition of the...

article

The HF-SCF energy of HIV-1 MNgp120 V3 hairpin loop conformers

Joel K. Weltman, Gail Skowron, George B. Loriot

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 367-372

The purpose of this study is to analyze the structure of the V3 loop of the HIV-1 gp120 molecule at the atomic level. The total energy of each member of the antibody-complexed 16-mer V3 conformer data set of Sharon et al. (PDB 1NJ0) was determined by the Hartree–Fock-self-consistent field (HF-SCF) method and with the GROMOS96 force field. There was no correlation between the results of the classical...

article

A DFT investigation of conformational geometries and interconversion equilibria of phenylthiosemicarbazone and its complexation with zinc

Vithaya Ruangpornvisuti, Banchob Wanno

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 418-426

The geometrical structures of phenylthiosemicarbazone (HAPhTSC) conformers have been obtained by geometry optimizations using density functional theory (DFT) calculations at the B3LYP/6-31G(d) and B3LYP/6-311G(d,p) levels of theory. Six thioamino and 24 thioimino tautomers of HAPhTSC have been found. Six tautomerization reactions between thioamino and thioimino tautomers occurring via transition states...

article

Determination of fuzzy logic membership functions using genetic algorithms: application to structure–odor modeling

Mohamed Kissi, Mohammed Ramdani, Mustapha Tollabi, Driss Zakarya

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 335-341

Fuzzy logic has been used as a tool in structure–camphoraceous odor relationships. The data base studied included 99 molecules. The rules used to discriminate between camphor and non camphor molecules lead to 77% correct discrimination. Such rules account for the shape and the size of the molecule. Their adjustment by means of genetic algorithms led to 84% correct discrimination between camphor and...

article

Modeling the helicase domain of Brome mosaic virus 1a replicase

Damià Garriga, Juana Dìez, Baldomero Oliva

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 382-392

Brome mosaic virus (BMV) is a representative member of positive-strand RNA viruses. The 1a replicase from BMV is a membrane protein of unknown structure with a methyltransferase N-terminal domain and a putative helicase activity in the C-terminal domain. In order to make a functional prediction of the helicase activity of the BMV 1a C-terminal domain, we have built a model of its structure. The use...

article

A method for structural analysis of α-helices of membrane proteins

Pranab K. Mohapatra, Adikanda Khamari, Mukesh K. Raval

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 393-398

A method has been developed to calculate and represent the geometry of α-helices of membrane proteins. Geometrical parameters are computed from coordinate files in the protein data bank. The axis of the helix is determined from the local centroids of tetrapeptide units of the helix. The method provides lower and upper cutoff values of the distance between backbone atoms C_i(carbonyl carbon) and N...

article

Predicting anti-HIV activity of 2,3-diaryl-1,3-thiazolidin-4-ones: computational approach using reformed eccentric connectivity index

Vipin Kumar, Satish Sardana, Anil Kumar Madan

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 399-407

The eccentric connectivity index, which has recently been employed successfully for the development of numerous mathematical models for the prediction of biological activities of diverse nature, has been reformed to overcome its limitations caused by degeneracy and insensitivity towards heteroatoms. The reformed eccentric connectivity index, termed the eccentric connectivity topochemical index, overcomes...

article

Closing loop base pairs in RNA loop–loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations

Jérôme Golebiowski, Serge Antonczak, Juan Fernandez-Carmona, Roger Condom, more

Journal of Molecular Modeling > 2004 > 10 > 5-6 > 408-417

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop–loop RNA duplexes neutralized by Mg²⁺ counterions in aqueous phases. Mismatches GA, CU and Watson–Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal...

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5-6
Volume:
10
Year:
2004

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Keywords

HOMOLOGY MODELING (2)
1A (1)
2, 3-DIARYL-1 (1)
3-THIAZOLIDIN-4-ONE (1)
ALZHEIMER’S DISEASE (1)
ANTI-HIV ACTIVITY (1)
ASPARTIC PROTEASE (1)
BENZODIAZEPINE (1)
BIOCATALYSIS MECHANISM (1)
BROME MOSAIC VIRUS (1)
DFT METHOD (1)
DRUG RESISTANCE (1)
ECCENTRIC CONNECTIVITY INDEX (1)
ECCENTRIC CONNECTIVITY TOPOCHEMICAL INDEX (1)
ENERGY (1)
ET ANALYSIS (1)
ETSA INDEX (1)
FUZZY LOGIC (1)
GENETIC ALGORITHMS (1)
GP120 (1)
HAPHTSC (1)
HELICASE (1)
HELIX PARAMETERS (1)
HF-SCF (1)
HINGE (1)
HIV-1 (1)
HYDROGEN BONDING (1)
INHIBITION (1)
INTERACTION ENERGY (1)
INTERCONVERSION (1)
KINK (1)
LID MOVEMENT (1)
LIGAND BINDING CORE (1)
LIPASE (1)
MISMATCH (1)
MODELING (1)
MOLECULAR DYNAMICS (1)
MOLECULAR DYNAMICS SIMULATION (1)
MOLECULAR ORBITALS (1)
NMDA (1)
OLFACTION (1)
ORGANIC SOLVENT (1)
PHENYLTHIOSEMICARBAZONE (1)
POTENTIAL ENERGY FUNCTION (1)
PRENYLATION (1)
PROTEIN–LIGAND DOCKING (1)
QSAR (1)
RNA (1)
S1S2 SEGMENT (1)
SCORING (1)
SIMULATION (1)
STRUCTURAL FLEXIBILITY (1)
STRUCTURE–ACTIVITY RELATIONSHIP (1)
SWIVEL (1)
TAUTOMERIZATION (1)
THREADING (1)
TOPOLOGICAL INDICES (1)
TRANSFERASES (1)
TRANSMEMBRANE HELIX (1)
V3 LOOP (1)
VIRTUAL SCREENING (1)
WIENER’S INDEX (1)
ZINC COMPLEX (1)
Γ-SECRETASE (1)
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