Eucb: A C++ program for molecular dynamics trajectory analysis

Abstract Eucb is a standalone program for geometrical analysis of molecular dynamics trajectories of protein systems. The program is written in GNU C++ and it can be installed in any operating system running a C++ compiler. The program performs its analytical tasks based on user supplied keywords. The source code is freely available from http://stavrakoudis.econ.uoi.gr/eucb under LGPL 3 license. Program summary Program title: Eucb Catalogue identifier: AEIC_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEIC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 31 169 No. of bytes in distributed program, including test data, etc.: 297 364 Distribution format: tar.gz Programming language: GNU C++ Computer: The tool is designed and tested on GNU/Linux systems Operating system: Unix/Linux systems RAM: 2 MB Supplementary material: Sample data files are available Classification: 3 Nature of problem: Analysis of molecular dynamics trajectories. Solution method: The program finds all possible interactions according to input files and the user instructions. Then it reads all the trajectory frames and finds those frames in which these interactions occur, under certain geometrical criteria. This is a blind search, without a priori knowledge if a certain interaction occurs or not. The program exports time series of these quantities (distance, angles, etc.) and appropriate descriptive statistics. Running time: Depends on the input data and the required options.

[1]  Mihaly Mezei,et al.  TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations , 2006, J. Comput. Aided Mol. Des..

[2]  P. Petrone,et al.  MHC-peptide binding is assisted by bound water molecules. , 2004, Journal of molecular biology.

[3]  Molecular Dynamics Simulations of the TSSPSAD Peptide Antigen in Free and Bound with CAMPATH-1H Fab Antibody States: The Importance of the β-Turn Conformation , 2009, International Journal of Peptide Research and Therapeutics.

[4]  Jan Hermans,et al.  Qmd‐plot: A graphical utility for rapid preliminary analysis of time series of fluctuating data, developed in the context of molecular dynamics simulations , 2002, J. Comput. Chem..

[5]  A. Stavrakoudis.  A disulfide linked model of the complement protein C8γ complexed with C8α indel peptide , 2009, Journal of molecular modeling.

[6]  G. Tóth,et al.  Stabilization of local structures by pi-CH and aromatic-backbone amide interactions involving prolyl and aromatic residues. , 2001, Protein engineering.

[7]  Nicholas M. Glykos,et al.  Software news and updates carma: A molecular dynamics analysis program , 2006, J. Comput. Chem..

[8]  Toon Verstraelen,et al.  MD-TRACKS: A Productive Solution for the Advanced Analysis of Molecular Dynamics and Monte Carlo simulations , 2008, J. Chem. Inf. Model..

[9]  W. Kabsch.  A solution for the best rotation to relate two sets of vectors , 1976 .

[10]  R. J. Yamartino,et al.  A Comparison of Several `Single-Pass' Estimators of the Standard Deviation of Wind Direction. , 1984 .

[11]  A. Glättli,et al.  Interpreting NMR Data for β-Peptides Using Molecular Dynamics Simulations , 2005 .

[12]  A. Stavrakoudis.  Computational modelling and molecular dynamics simulations of a cyclic peptide mimotope of the CD52 antigen complexed with CAMPATH-1H antibody , 2010 .

[13]  A. Stavrakoudis,et al.  Molecular dynamics simulation of antimicrobial peptide arenicin‐2: β‐Hairpin stabilization by noncovalent interactions , 2009, Biopolymers.

[14]  Insights into the structure of the PmrD protein with molecular dynamics simulations. , 2009, International journal of biological macromolecules.

[15]  A. Stavrakoudis.  Conformational Studies of the 313-320 and 313-332 Peptide Fragments Derived from the αIIb Subunit of Integrin Receptor with Molecular Dynamics Simulations , 2009, International Journal of Peptide Research and Therapeutics.

[16]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[17]  A. Bax,et al.  Reparametrization of the Karplus Relation for 3J(H.alpha.-N) and 3J(HN-C') in Peptides from Uniformly 13C/15N-Enriched Human Ubiquitin , 1995 .