Software

SuAVE (Surface Assessment Via grid Evaluation)

The program SuAVE (Surface Assessment Via grid Evaluation) is a Fortran-based program developed to analyze geometrical and physical properties of surfaces taking into account the structural morphology of the systems. It relies on the application of a radial base function to interpolate points scattered across an interface of any shape enabling the representation of the chemical interface as fully differentiable so that related geometrical properties can be calculated through the straightforward employment of well-established differential geometry techniques. If you find any issue please drop us an email. If you make use of the software for you research, please cite: Santos, D. E. S.; Pontes, J. F. S.; Lins, R. D.; Coutinho, K.; Soares, T. A. (2019) SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces. Journal of Chemical Information and  Modeling. Accepted for publication. DOI: 10.1021/acs.jcim.9b00569.

Web Tools

IMS Peptider

 

A proteomics tool that predicts the primary sequence of a peptide from IMS/MS data.

Rotational Profiler

 

This webtool fits a MM calculated torsional profile to its QM calculated reference.

 

 

 

          Parameters and Topologies

 

Parameters for simulations of Polymixin B and different LPS chemotypes of P. aeruginosa

 

This file contains the topologies and coordinates for Polymixin B and different LPS chemotypes of the Gram-negative bacteria P. aeruginosa, namely, Lipid A, Lipid A modified with 4-amino-4-deoxy-L-arabinose (hexa- and pentaacylated species) and LPS Re (pentaacylated species). The membrane coordinates have been equilibrated for 200 ns. These files are expected to be error-free, but please do check them for errors. If you find any issue please drop us an email. If you make use of the topologies and/or atomic coordinates for you research, please cite: Santos, D. E. S. ; Pol-Fachin, L. ; Lins, R. D. ; Soares, T. A. (2017) Polymyxin Binding to the Bacterial Outer Membrane Reveals Cation Displacement and Increasing Membrane Curvature in Susceptible but not in Resistant LPS Chemotypes. Journal Chem. Inf. and Model. DOI: 10.1021/acs.jcim.7b00271

 

Parameters for simulation of Lipid A membranes (P. aeruginosa)

This file contains the topologies and coordinates of Lipid A (hexa- and pentaacylated species) for Pseudomonas aeruginosa bacteria. The force field is a extension of the GROMOS force field combinated with the 45a4 carbohydrate parameter set and are in the GROMACS format of topologies. These files are expected to be error-free, but please do check them for errors. If you find any issue please drop us an email. If you make use of the topologies and/or atomic coordinates for you research, please cite Frederico J. S. Pontes , Victor H. Rusu , Thereza A. Soares, and Roberto D. Lins. Journal Chem. Theory Compu.(2012), v. 8 (10), p. 3830–3838 DOI: 10.1021/ct300084v"

Glycam-based parameters for simulating LPS membranes

 

 

The force field, topologies and coordinate files for the 650-ns equilibrated LPS membrane are freely available for download. The atomic coordinates in PDB format can be visualized in with most molecular graphics programs such as VMD, PyMol, and alike. The force field and topology files are compatible with the GROMACS suite of programs. These files are expected to be error-free, but please do check them for errors. If you find any issue please drop us an email. If you make use of the topologies and/or atomic coordinates for you research, please cite Kirschner, Lins, Maass, Soares. 2012. Journal Chem. Theory Comp. (2012). DOI: 10.1021/ct300534j.

GROMOS 45A4 parameter file extension to chitin and chitosan

Compatible with GROMOS 56A6 and 53A7 parameter files. Please read and cite: Journal Chem. Theory Compu. (2008), v. 4, p. 2141-2149, and Biopolymers (2011), v. 95, p. 448-460, DOI: 10.1002/bip.21602

GROMOS 53A6glyc parameters for aldohexopyranose-based carbohydrates

The residue topology parameters for sixteen aldohexopyranoses, in the GROMACS format of topologies, are freely available for download in this file. Such force field, named GROMOS 53A6glyc, is an improvement of the GROMOS 45A4 carbohydrate parameter set, being compatible with GROMOS 53A6 and 54A7 force field for other classes of biomolecules. These files are expected to be error-free, but please do check them for errors. If you find any issue please drop us an email. If you make use of the topologies for your research, please cite Laercio Pol-Fachin, Victor Holanda Rusu, Hugo Verli, and Roberto D. Lins. J. Chem. Theory Comput., 2012, 8(11), 4681-4690. DOI: 10.1021/ct300479h