13,352 Result(s)
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Molecular Medicine
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Chemistry
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Article
AdaptivSearch: A Novel Iterative Algorithm for the Generation of n-dimensional Hypersurfaces Using an Adaptive Numerical Strategy
AdaptivSearch is the first adaptive strategy based algorithm for the rational and economical construction of n-dimensional hypersurfaces. AdaptivSearch works iteratively: At each step it parcels out the definiti...
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Comparison of a Homology Built Model of Angiogenin to its Crystal Structure
The comparison of our homology built model of human angiogenin with the recently determined x-ray structure of the same is reported. The basic details of the structure in terms of alpha -helices and beta shee...
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Molecular Dynamics of the Ha-ras Protein: Nucleotide Atom-Centred Charges within the AMBER Force Field
Molecular dynamics simulations have become an essential tool for the study of biological systems. The Ha-ras protein, is a system suitable for such studies. Despite much recent progress, it is still not known ex...
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Ergoline Derivatives as a Probe for Featuring the 5-HT1A Receptor Pharmacophore
A 5-HT1A pharmacophore has been obtained employing a set of rigid templates encompassing the 5-HT1A structure. The use of rigid templates allowed us to overcome the discrepancy found when flexible structures whe...
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A Detailed Study of VESPA Electrostatic Potential-Derived Atomic Charges
VESPA, an improved semiempirical method for the calculation of electrostatic potential-derived atomic charges has been tested. It is shown that this approach is even less dependent upon molecular orientation ...
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A Hybrid Density Functional-Classical Molecular Dynamics Simulation of a Water Molecule in Liquid Water
A hybrid NVE Molecular Dynamics simulation of liquid water is presented using a coupled Density Functional/Molecular Mechanics hamiltonian. The quantum subsystem is a single water molecule described by means ...
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A ′Fragment Fitting Approach′ to Model Disulfide Loops by Utilizing Homologous Peptide Fragments from Unrelated Proteins of Known Structures: Application to the V3 Loop of the HIV-1 Envelope Glycoprotein gp120
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Molecular Mechanics: The Conjugate Nitro Group Parameters in the MM2 Force Field
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Identification of Helical Packing Motifs Common to Bacteriorhodopsin and G Protein-Coupled Receptors
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Similarity Study on Peptide γ-turn Conformation Mimetics
The ability of a series of structures to mimic the geometric and electronic properties of an ideal γ–turn has been studied. Initially, an exhaustive conformational analysis was carried out using the molecular ...
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Article
Theoretical Methods for the Representation of Solvent
A review of the theoretical approaches for the representation of the solvent effect on molecular structure and reactivity is presented. The main characteristics of the different methods available for the descr...
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Article
Structural Evaluation of Distant Homology. A 3-D Model of the Ligand Binding Domain of the Nicotinic Acetylcholine Receptor Based on Acetylcholinesterase: Consistency with Experimental Data
Acetylcholine is a ligand for both acetylcholinesterases and nicotinic acetylcholine receptors. Hence, at least some local sequence and structural similarities between the acetylcholinesterases and the recepto...
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Article
The Erythrocyte/Brain Glucose Transporter (GLUT1) May Adopt a Two–Channel Transmembrane α/β Structure.
There are two models of topology for the membrane domains of the erythrocyte/brain facilitative glucose transporter, GLUT1. The first is composed of 12 membrane–spanning α–helices, the second of 16 membrane-sp...
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Conformational Behavior and Flexibility of Terminally Blocked Cysteine and Cystine
Conformational potential energy hypersurfaces, PES, for the terminally blocked L-Cysteine, L,L-Cystine and D,L-Cystine have been analyzed by means of molecular mechanics in combination with the programs ROSE, CIC...
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A Semiempirical Transition State Structure for the First Step in the Alkaline Hydrolysis of Cocaine. Comparison between the Transition State Structure, the Phosphonate Monoester Transition State Analog, and a Newly Designed Thiophosphonate Transition State Analog
Semiempirical molecular orbital calculations have been performed for the first step in the alkaline hydrolysis of the neutral benzoylester of cocaine. Successes, failures, and limitations of these calculations...
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Article
Molecular Parameterisation and the Theoretical Calculation of Electrode Potentials
The difference in reduction potentials between ortho and para-benzoquinones has been calculated. The employs gas phase ab initio and semi-empirical computations in combination with free energy perturbation theory...
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Article
Davydov Soliton Dynamics in Proteins: II. The General Case
We performed long time simulations using the |D1> approximation for the solution of the Davydov Hamiltonian. In addition we computed expectation values of the relevant operators with the state (Ĥ ...
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Article
Davydov Soliton Dynamics in Proteins: I. Initial States and Exactly Solvable Special Cases
For the Davydov Hamiltonian several special cases are known which can be solved analytically. Starting from these cases we show that the initial state for a simulation using Davydov′s |D1> approximation has to be...
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Article
Substrate Specifity of Chymotrypsin. Study of Induced Strain by Molecular Mechanics
Acylenzyme intermediates, produced by transfer of the acyl portions of selected natural substrates onto the catalytic serine hydroxyl of the serine protease chymotrypsin, were modeled with the AMBER force fiel...
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Article
Solvation Effects on the Conformational Behaviour of Gellan and Calcium Ion Binding to Gellan Double Helices
The contribution of the presence of solvent to the conformations adopted by disaccharide fragments within the repeat unit of gellan have been studied by molecular modelling techniques. Initial conformational e...
