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Indice del Software

Modelo de red torsional (TNM)

TNM

Program that computes the normal modes of the torsional network model (TNM), an elastic network model whose degrees of freedom are the torsion angles of the protein backbone. These modes displace backbone atoms including C β maintaining their covalent geometry.

  • Versión : 1.0. Uso gratuito para fines educacionales y de investigación.
  • Contactar con : ubastolla@cbm.csic.es
  • Acceso : Aquí.
  • Referencia : Raul Mendez and Ugo Bastolla - PRL 104, 228103 (2010)

Análisis de estabilidad de proteínas

DeltaGREM

Computes the folding free energy of proteins with known structure. Sequences can be input either through a Multiple Sequence Alignment including the sequence of at least one of the input PDB or through a list of mutations.

The folding free energy takes into account the native state as represented in one of the input PDB files, the unfolded state, and the misfolded state (compact conformations dissimilar from the native), modelled as a Random Energy Model (REM) up to the second (REM2) or third (REM3) moment of the contact energy.

  • Versión : 1.0 Uso gratuito para fines educacionales y de investigación.
  • Contactar con : ubastolla@cbm.csic.es
  • Acceso : Aquí.
  • Referencia : Minning J, Porto M, Bastolla U. Proteins. 2013 Jul;81(7):1102-12.

Comparación de estructuras de proteínas

Contact_divergence

Calcula divergencias en secuencia y estructura de proteínas homologas con estructuras conocidas. Dado un alineamiento multiple, para todos los pares de proteinas calcula la divergencia en secuencia de Tajima-Nei, la divergencia de contactos (Pascual-Garcia et al. 2010) y la divergencia del TM-score (Zhang and Skolnick 2005) -log(TM). Fichero de entrada: alineamiento multiple de secuancias en formato fasta con nombres de ficheros pdb como nombres de proteinas, opcionalmente seguidos por codigos de cadena (Ex: >1opd.pdb A). La primera linea indica el directorio de los ficheros PDB, PDBDIR= (default: current directory).

  • Versión : 1.0 Uso gratuito para fines educacionales y de investigación
  • Contactar con : ubastolla@cbm.csic.es
  • Acceso : Aquí.
  • Referencia : Pascual-García A, Abia D, Méndez R, Nido GS, Bastolla U. Proteins. 2010 78:181-96.

MAMMOTH

MAMMOTH (Matching Molecular Models Obtained from Theory) es un mátodo de alineamiento estructural de proteínas independiente de su secuencia. Esto permite la comparación de la estructura experimental de una proteína con un modelo arbitrario de baja resolución. También permite la comparación de dos estructuras experimentales, así como la búsqueda de estructuras similares en una base de datos.

  • Versión : Uso gratuito para fines educacionales y de investigación
  • Contactar con : ub@cbm.csic.es
  • Acceso : Aquí.
  • Referencia : Ortiz AR, Strauss CE, Olmea O (2002) Protein Sci. 11:2606-21.

MAMMOTH-mult

MAMMOTH-mult es una versión de alineamiento múltiple de MAMOTH. Realiza alineamientos múltiples de proteínas proporcionando una superposición 3D, el consecuente alineamiento de secuencia basado en estructura, así como un dendograma para el conjunto de estructuras alineadas.

  • Versión : 1.0 Uso gratuito para fines educacionales y de investigación
  • Contactar con : ub@cbm.csic.es
  • Acceso : Aquí.
  • Referencia : Lupyan D, Leo-Macias A, Ortiz AR (2005) Bioinformatics (2005) 21, 3255-63

Evolución Molecular

ProtEvol

    The program ProtEvol performs two kinds of computation:

    1. It computes the mean-field site-specific amino acid distributions that have minimal differences with respect to the background distribution and that constraint the average stability of the native state of the protein against both unfolding and misfolding. The program also computes an exchangeability matrix derived from an empirical substitution model or from a mutation model that can be used together with the site-specific distributions for applications in phylogenetic inference. Citation: Arenas, Sanchez-Cobos and Bastolla, Maximum likelihood phylogenetic inference with selection on protein folding stability,

    2. It simulates protein evolution subject to the constraint of selection on the folding stability of the native state of the protein against both unfolding and misfolding. It implements three selection models:
      1. Neutral;
      2. Based on the fixation probability of the Moran process, which depends on the difference of logarithmic fitness and on effective population size.
      3. Based on the mean-field stationary distributions computed at the previous point.

  • Instalación Documentación incluida en el paquete.
  • Licencia : Uso gratuito para fines educacionales y de investigación.
  • Contactar con : ubastolla@cbm.csic.es
  • Referencia : Arenas M, Sánchez-Cobos A, Bastolla U. Mol Biol Evol. 2015 32:2195-207.
  • Descargar : Es necesario registrarse primero.

ProteinEvolver

ProteinEvolver generates samples of protein-coding genes and protein sequences evolved along phylogenies under structure-based substitution models. These models consider the protein structure to evaluate candidate mutations, which can be accepted (substitutions) or rejected depending on the energy of the protein structure of the mutated sequence. The simulation of molecular evolution occurs along phylogenetic histories, which can be either user-specified or simulated by the coalescent modified with recombination (including recombination hotspots), migration, demographics and longitudinal sampling.

Diseño de fármacos (Dr. Antonio Morreale y colaboradores)

MM-ISMSA

A Scoring Function for Protein-Protein and Protein-Ligand Docking and Molecular Dynamics.

  • Versión : 0.8
  • Acceso : Aquí.
  • Contactar con : ub@cbm.uam.es
  • Referencia :
    1. Javier Klett, Alfonso Núñez-Salgado, Helena G. Dos Santos, Álvaro Cortés-Cabrera, Almudena Perona, Rubén Gil-Redondo, David Abia, Federico Gago, and Antonio Morreale
      MM-ISMSA: an ultra-fast and accurate scoring function for protein-protein docking. J. Chem. Theory Comput., 8, 3395-3408 (2012)
    2. Morreale, A.; Gil-Redondo, R.; Ortiz, A.R. A new implicit solvent model for protein-ligand docking. Proteins 2007 May, 67: 606-16.

gCOMBINE

A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes.

  • Versión : 1.2
  • Acceso : Aquí.
  • Contactar con : ub@cbm.uam.es
  • Referencia :
    1. A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes. Gil-Redondo R,Klett J, Gago F, Morreale A. Proteins 2010; 78(1):162-72
    2. Prediction of drug binding affinities by comparative binding energy analysis. Ortiz AR, Pisabarro MT, Gago F, Wade RC. J Med Chem 1995; 38:2681-91.
    3. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design. Perez C, Pastor M, Ortiz AR, Gago F. J Med Chem. 1998:41(6):836-52

CRDOCK

CRDOCK is a protein-ligand docking program similar to Glide, DOCK or Autodock. It uses a hybrid scoring function based on GlideScore(tm) using a molecular mechanics energy function (AMBER-like) and the ChemScore function to score interactions. The docking program is particularly well suited to generate molecular models of ligand-receptor complexes for further use in COMBINE analysis.

  • Versión : 0.8
  • Acceso : Aquí.
  • Contactar con : Antonio Morreale(antonio.morreale@repsol.com)
  • Referencia : Cabrera, A.C.; Klett, J.; Dos Santos, H. G.; Perona, A.; Gil-Redondo, R.; Francis, S. M.; Priegos, E. M.; Gago, F.; Morreale, A.; CRDOCK: An Ultrafast Multipurpose Protein–Ligand Docking Tool (2012) Journal of Chemical Information and Modeling (in press)

VSDMIP

VSDMIP es una plataforma para el cribado virtural de quimiotecas, integrada en una base de datos relacional MySQL.

  • Versión : 1.0
  • Licencia : La plataforma se distribuye gratuitamente para uso académico y de investigación, bajo petición a los authores.
  • Contactar con : Antonio Morreale (antonio.morreale@repsol.com)
  • Acceso : Aquí
  • Referencia :
    1. Rubén Gil-Redondo, Jorge Estrada, Antonio Morreale, Fernando Herranz, Javier Sancho, and Ángel R. Ortíz. VSDMIP: Virtual Screening Data Management on an Integrated Platform J. Comput.-Aided Mol. Design, 23, 171-184 (2009);
    2. Álvaro Cortés-Cabrera, Rubén Gil-Redondo, Almudena Perona, Federico Gago, and Antonio Morreale. VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface. J. Comput.-Aided Mol. Design, 25, 813-824 (2011)

cGRILL: a simple affinity map generator

cGRILL calculates 4 affinity maps: lipophilic (CH3), hydrogen bond acceptor (=O), hydrogen bond donor (NH4+) and mixed hydrogen bond donor-acceptor (OH). It implements AMBER force field van der Waals and electrostatic terms and a custom hydrogen bond. The code is not pretty but it is licensed under GPL v3.

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