EletroGrid:

Calcula o potencial eletrostático em uma carga de prova, pela lei de Coulomb, em uma rede de pontos no espaço no entorno de uma molécula.

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HbMap2grace:

Description will be available soon.

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Porcupine

Show the vectors obtained from molecular dynamics principal component analysis, or from normal modes, using the VMD program.

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SurfinMD:

SurfinMD can be used to calculate the surface of contact between a drug and a protein, separating the results by diferent properties and by amino-acid residues.

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Rsurf2Grace:

Rsurf2Grace is a tool that make it easy to generate surface of contact plots, using the XmGrace program. This tool is very useful to better analyse the results from SurfinMD.

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GSAFold: Protein Structure Prediction

The structure determines proteins activity and properties; thus knowing such conformation on an atomic level is essential for both basic and applied studies of protein function and dynamics. GSAFold applies the generalized simulated annealing (GSA) algorithm on ab initio protein structure prediction. The GSA is a stochastic search algorithm employed in energy minimization and used in global optimization problems, especially those that depend on long-range interactions, such as gravity models and conformation optimization of small molecules. This new implementation applies, for the first time in ab initio protein structure prediction, an analytical inverse for the Visitation function of GSA. It also employs the broadly used NAMD Molecular Dynamics package to carry out energy calculations, allowing the user to select different force fields and parameterizations. Moreover, the software also allows the execution of several simulations simultaneously. Applications that depend on protein structures include rational drug design and structure-based protein function prediction.

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Trj2PDB:

Converte trajetórias de simulação de dinâmica molecular no formato TRJ, adotado pelo programa NWChem, para trajetórias no formato PDB, universalmente aceito pelos programas de analise de simulação.

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GAMINI:

Description will be available soon.

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GANMD:

Description will be available soon.

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ss2grace:

Description will be available soon.

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THOR:

Description will be available soon.

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THOR/GSA:

Description will be available soon.

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Success stories:

GSAFold - Mastoparan-X

The simulation with the peptide mastoparan-X took seven days to calculate simultaneously 500,000 minimization steps for 200 structures (each with a unique seed for the random number generator) in a Dual Intel Xeon E5504 machine, significantly faster than previous works using Monte Carlo or MD especially when one observes the necessary number of steps to obtain the native folded conformation. Regarding the accuracy of the structure predicted, there are 14 experimental structures available in the PDB for the mastoparn-X (PDB entry: 1A13) and each of this structures were compared to those generated using the GSAFold, by analyzing the RMSD between them. Figure 1 shows the results in a graph relating each final structure with its mean RMSD, which is a measure of how similar are the structures being compared. The best RMSD found was of 3.00Å , indicating a good agreement with the experiment, as showed in the Figure bellow.

Porcupine - Potassium Channel

We have investigated by MD simulations the anesthetic effect, specifically its interaction with the biological membrane and a potassium channel. The PCA analysis showed a twist movement of the transmembrane helixes that opens the channel.

Porcupine - β1-adrenoceptor

The human β1-adrenoceptor is a transmembrane protein responsible for the signal transduction pathway via agonist interaction. Despite its importance, β1 activation mechanism is still unclear. The most studied and widely accepted mechanism is the disruption of a salt bridge between TM3 arginine and TM6 glutamic acid, called ionic lock. Porcupine plot of principal mode analysis shows that the combined motions of the 7TM motif are opposites in each side (intracellular and extracellular) of the receptor and they have different intensitie. From the intracellular point of view, the amplitude of the motions of the extracellular domain in the clockwise direction is greater than the counter-clockwise movement of the inner receptor moiety.