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Modelling protein structures

Description:

Modelling unknown protein structures from sequence, using standard algorithms and algorithms developed in our group. The price may vary depending on the number of domains to predict and the sequence similarity with the template protein, since remote similarity require more sophisticated and time consuming methods.

Internal price: 60 €
External academic: 120 €
External non-academic: 180 €
Online demand

Modelling conformational changes of proteins with known structure.

Description:

We model conformational changes through the largest amplitude normal modes predicted using the elastic network model (ENM developed by us) which uses torsion angles as degrees of freedom and can be solved analytically in very short computational time.

Internal price: 30 €
External academic: 60 €
External non-academic: 90 €
Online demand

Molecular dynamics of proteins

Description:

We can simulate protein dynamics through molecular dynamics using realistic force fields. In this way, we can also predict interaction energies for protein complexes.

Internal price: 100 € * (SimulationTime (ns)/5 + ProteinLength (AA)/100)
External academic: 150 € * (SimulationTime (ns)/5 + ProteinLength (AA)/100)
External non-academic: 200 € * (SimulationTime (ns)/5 + ProteinLength (AA)/100)
Online demand

Predicting protein folding stability

Description:

Given a protein sequence with known structure (or with a structure that can be reliably predicted) we can predict its stability with respect to unfolding and with respect to missfolded structures using our own algorithm. Furthermore, we can predict its tendency to be natively unfolded, using the algorithm disopred2 by David Jones, and its tendency to aggregate, using the algorithm TANGO by Luis Serrano

Internal price: 30 €
External academic: 60 €
External non-academic: 90 €
Online demand

Generating multiple alignments and dendrograms

Description:

We can generate multiple alignments and dendrograms from either protein sequences or protein structures. For sequences, we shall use the algorithm MUSCLE or algorithms based on Hidden Markov Models. For protein structures we shall use the algorithm MAMMOTHmult, developed at our laboratory. From these alignments, we can derive a tree expressing the evolutionary relationships between the proteins. The sequences subject to the alignment may be retrieved through a BLAST or PSI-BLAST search from a query protein.(10€, additional fee)

Internal price:
Sequence alignment: 15€ up to 500 proteins, consult for more.
Structure alignment: 20€ up to 20 proteins, cosult for more.
External academic:
Sequence alignment: 30€ up to 500 proteins, consult for more.
Structure alignment: 40€ up to 20 proteins, cosult for more.
External non-academic:
Sequence alignment: 45€ up to 500 proteins, consult for more.
Structure alignment: 60€ up to 20 proteins, cosult for more.
Online demand

Other problems in computational biology

Description:

We are open for giving advice about almost all kinds of problems in computational biology.

Internal price: Advice free, analysis 10 €/h.
External academic: 20€/h plus 1 €/CPU h.
External non-academic: 40€/h plus 2 €/CPU h.
Online demand

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