Software Index

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.

• Version : 1.0. Free use for Educational and Research Purposes.
• Contact : ubastolla@cbm.csic.es
• Access : Here.
• References : Raul Mendez and Ugo Bastolla - PRL 104, 228103 (2010)

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.

• Version : 1.0 Free use for Educational and Research Purposes.
• Contact : ubastolla@cbm.csic.es
• Access : Here.
• References : Minning J, Porto M, Bastolla U. Proteins. 2013 Jul;81(7):1102-12.

Contact_divergence

Computes sequence and structure divergence measures of homologous proteins with known structures. Given a multiple sequence alignment, for all pairs of proteins it computes the Tajima-Nei sequence divergence, the contact divergence (Pascual-Garcia et al. 2010) and the TM-score (Zhang and Skolnick 2005) divergence -log(TM). Input: alignment file in fasta format with names of pdb files as file names, optionally followed by the chain index (Ex: >1opd.pdb A) The first line may be PDBDIR= (default: current directory).

• Version : 1.0 Free use for Educational and Research Purposes.
• Contact : ubastolla@cbm.csic.es
• Access : Here.
• References : Pascual-García A, Abia D, Méndez R, Nido GS, Bastolla U. Proteins. 2010 78:181-96.

MAMMOTH

MAMMOTH (Matching Molecular Models Obtained from Theory) is a sequence-independent protein structural alignment method. It allows the comparison of an experimental protein structure with an arbitrary low-resolution protein tertiary model. It also allows the comparison of two experimental structures, or the search for similar structures to a query structure in a database.

• Version : Free use for Educational and Research Purposes.
• Contact : ub@cbm.csic.es
• Access : Here.
• References : Ortiz AR, Strauss CE, Olmea O (2002) Protein Sci. 11:2606-21.

MAMMOTH-mult

MAMMOTH-mult is a multiple alignment version of MAMMOTH. It multiply aligns protein structures, providing a common 3D superimposition, a corresponding structure-based sequence alignment and a dendrogram for the set of structures aligned.

• Version : 1.0 Free use for Educational and Research Purposes.
• Contact : ub@cbm.csic.es
• Access : Here.
• References : Lupyan D, Leo-Macias A, Ortiz AR (2005) Bioinformatics (2005) 21, 3255-63

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.


• Usage and installation Documentation included with the package.
• License : Free use for Educational and Research Purposes.
• Contact : ubastolla@cbm.csic.es
• References : Arenas M, Sánchez-Cobos A, Bastolla U. Mol Biol Evol. 2015 32:2195-207.
• Download : register or login

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.

• Version: 1.0
• Usage and installation : Documentation included with the package.
• Examples : included with the package.
• Contact : ubastolla@cbm.csic.es
• License : Free use for Educational and Research Purposes.
• Download : Google Code.
• References : Arenas, M.; Dos Santos, H.G.; Posada, D. and Bastolla, U. (2013) Bioinformatics, 29(23):3020-3028.

MM-ISMSA

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

• Version : 0.8
• Access : Here.
• Contact : ub@cbm.uam.es
• References :
  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.

• Version : 1.2
• Access : Here.
• Contact : ub@cbm.uam.es
• References :
  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.

• Version : 0.8
• Access : Here.
• Contact : Antonio Morreale(antonio.morreale@repsol.com)
• References : 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 is a platform for virtual screening (VS) of chemical libraries, integrated within a MySQL relational database.

• Version : 1.0
• License : The software is freely distributed for academic and research purposes upon request to the authors.
• Contact : Antonio Morreale (antonio.morreale@repsol.com)
• Access : Here
• References :
  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.

• Access : Here