Algorithms, developments and applications in molecular modelling: the GAMESS-UK Ab Initio code

1999 ◽  
Author(s):  
M. F. Guest ◽  
H. J. J. van Dam
Keyword(s):  
Ab Initio ◽  
Molecular Modelling

scholarly journals Proteomic analysis and molecular modelling characterize the iron-regulatory protein haemojuvelin/repulsive guidance molecule c

2013 ◽  
Vol 452 (1) ◽  
pp. 87-95 ◽  
Author(s):  
Mahta Nili ◽  
Larry David ◽  
Johannes Elferich ◽  
Ujwal Shinde ◽  
Peter Rotwein
Keyword(s):  
Ab Initio ◽  
Molecular Modelling ◽  
Electron Transfer Dissociation ◽  
Structural Information ◽  
Regulatory Protein ◽  
Structural Features ◽  
Single Chain ◽  
Disulfide Linkages ◽  
Repulsive Guidance Molecule ◽  
Guidance Molecule

HJV (haemojuvelin) plays a key role in iron metabolism in mammals by regulating expression of the liver-derived hormone hepcidin, which controls systemic iron uptake and release. Mutations in HJV cause juvenile haemochromatosis, a rapidly progressing iron overload disorder in humans. HJV, also known as RGMc (repulsive guidance molecule c), is a member of the three-protein RGM family. RGMs are GPI (glycosylphosphatidylinositol)-linked glycoproteins that share ~50% amino acid identity and several structural motifs, including the presence of 14 cysteine residues in analogous locations. Unlike RGMa and RGMb, HJV/RGMc is composed of both single-chain and two-chain isoforms. To date there is no structural information for any member of the RGM family. In the present study we have mapped the disulfide bonds in mouse HJV/RGMc using a proteomics strategy combining sequential MS steps composed of ETD (electron transfer dissociation) and CID (collision-induced dissociation), in which ETD induces cleavage of disulfide linkages, and CID establishes disulfide bond assignments between liberated peptides. The results of the present study identified an HJV/RGMc molecular species containing four disulfide linkages. We predict using ab initio modelling that this molecule is a single-chain HJV/RGMc isoform. Our observations outline a general approach using tandem MS and ab initio molecular modelling to define unknown structural features in proteins.

Robust molecular representations for modelling and design derived from atomic partial charges

2016 ◽  
Vol 52 (4) ◽  
pp. 681-684 ◽  
Author(s):  
A. R. Finkelmann ◽  
A. H. Göller ◽  
G. Schneider
Keyword(s):  
Ab Initio ◽  
Molecular Modelling ◽  
Partial Charge ◽  
Partial Charges

Ab initio partial charge schemes are identified for molecular modelling purposes, and potential pitfalls of their application are discussed.

Theoretical studies on the propulsive and explosive performance of strained polycyclic cage compounds

2017 ◽  
Vol 41 (3) ◽  
pp. 920-930 ◽  
Author(s):  
Lovely Mallick ◽  
Sohan Lal ◽  
Sasidharakurup Reshmi ◽  
Irishi N. N. Namboothiri ◽  
Arindrajit Chowdhury ◽  
...  
Keyword(s):  
Ab Initio ◽  
Molecular Modelling ◽  
Theoretical Studies ◽  
Cage Compounds ◽  
Explosive Performance ◽  
Polycyclic Cage Compounds ◽  
Carbon Based

Carbon-based cage compounds could be better candidates as propellant ingredients than the currently used ones as per molecular modellingab initiocalculations.

Ab initio band theory approach to electron energy loss near edge structures

1988 ◽  
Vol 46 ◽  
pp. 506-507
Author(s):  
Xudong Weng ◽  
O.F. Sankey ◽  
Peter Rez
Keyword(s):  
Ab Initio ◽  
Local Density ◽  
Interpolation Method ◽  
Atomic Orbital ◽  
Plane Waves ◽  
Large Set ◽  
Theory Approach ◽  
Band Theory ◽  
Atomic Orbitals ◽  
Pseudopotential Calculations

Single electron band structure techniques have been applied successfully to the interpretation of the near edge structures of metals and other materials. Among various band theories, the linear combination of atomic orbital (LCAO) method is especially simple and interpretable. The commonly used empirical LCAO method is mainly an interpolation method, where the energies and wave functions of atomic orbitals are adjusted in order to fit experimental or more accurately determined electron states. To achieve better accuracy, the size of calculation has to be expanded, for example, to include excited states and more-distant-neighboring atoms. This tends to sacrifice the simplicity and interpretability of the method.In this paper. we adopt an ab initio scheme which incorporates the conceptual advantage of the LCAO method with the accuracy of ab initio pseudopotential calculations. The so called pscudo-atomic-orbitals (PAO's), computed from a free atom within the local-density approximation and the pseudopotential approximation, are used as the basis of expansion, replacing the usually very large set of plane waves in the conventional pseudopotential method. These PAO's however, do not consist of a rigorously complete set of orthonormal states.

An ab initio study of Se-reacted GaAs(0 0 1) surfaces

1998 ◽  
Vol 184-185 (1-2) ◽  
pp. 80-84 ◽  
Author(s):  
W Faschinger
Keyword(s):  
Ab Initio ◽  
Ab Initio Study
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