Francesco Rao Research Lab
Posted: June 18, 2011 Filed under: Uncategorized 1 Comment »We have a new homepage!
Go here, to get in touch with our research, publications, people and software development!
Pynoramix is released!
Posted: June 17, 2011 Filed under: Uncategorized Leave a comment »
PYNORAMIX is a software to analyze molecular dynamics trajectories of water. It offers a python-based framework to investigate water structure and dynamics, using complex network analysis.
A sample result is found here.
Go to github to get the latest release!
Twitter from the terminal
Posted: June 3, 2008 Filed under: Uncategorized | Tags: geek Leave a comment »This is huge. Send Twitter text from your burning terminal. For doing this, use curl:
#!/bin/bash
if [ "$1" == "" ]; then
echo " twitter message missing!"
exit
fi
USER=XXX
PASSWD=YYY
message=$*
curl -u $USER:$PASSWD -d status="$message" http://twitter.com/statuses/update.xml > /dev/null
If you don’t have curl just type in ubuntu:
sudo aptitude install curl
and you are there.
Also heard that you can do the same stuff using wget.
Power-law random generator
Posted: June 2, 2008 Filed under: Uncategorized Leave a comment »So you want to generate random numbers distributed along a power-law, uh?
Suppose your target distribution is:
you will use:
where x is a random variable distributed uniformly and n>1.
This formula comes from the differential equality:
which becomes:
in case x is distributed uniformly. For example, suppose you want to generate numbers which are distributed exponentially, you will use:
which finally gives:
Cell-cycle in short
Posted: February 7, 2008 Filed under: biology, cdks, cell_cycle Leave a comment »[This article is based on the Cell cycle wikipedia entry]
The cell cycle is the series of events that take place in a eukaryotic cell leading to its replication. These events can be divided in two periods: interphase (I) where the cell grows, accumulating nutrients needed for mitosis and duplicating its DNA and the mitotic (M) phase, during which the cell splits itself into two distinct cells. The interphas is divided in Gap1 (G1), Synthesis (S) and Gap2 (G2). Here it is a sketch (from nih):
The various stages of interphase are not usually morphologically distinguishable, on the other hand, they are characterized by different and distinct set of biochemical processes. In the S sub-phase DNA synthesis commences; when it is complete, all of the chromosomes have been replicated, i.e., each chromosome has two (sister) chromatids. Thus, during this phase, the amount of DNA in the cell has effectively doubled, though the ploidy of the cell remains the same.
Regulation of the cell cycle involves steps crucial to the cell, including detecting and repairing genetic damage, and provision of various checks to prevent uncontrolled cell division. The molecular events that control the cell cycle are ordered and directional; that is, each process occurs in a sequential fashion and it is impossible to “reverse” the cycle.
A Nobel prize was awarded in 2001 for their discovery of these central molecules.
Instantaneously generation of random numbers
Posted: February 5, 2008 Filed under: bash, geek, scripting Leave a comment »#! /bin/bash
coff=1.2
nnce=765
cent=cl_$coff.centers
seed=`date +'%N'`
awk 'BEGIN{
srand("'$seed'")
print int(rand())
}'
Trajectory overlay with VMD
Posted: January 29, 2008 Filed under: clusterization, geek, vmd 1 Comment »In Molecular Dynamics, especially when small fluctuations are involved, it can be helpful to display the snapshots contained in a trajectory all at once instead of viewing a movie. The same utility can be used, for example, to display the members of a structural cluster (you can generate clusters of structures using wordom).
This feature is usually achieved “by hand”, e.g., extracting all the snapshots of a trajectory into separate pdb files and then loading them all at once. A simple consequence of this, of course, is to have your hard-drive overfilled with redundant files.
Good for us, VMD is able to overlay in a single frame all the snapshots contained in your trajectory (thanks Riccardo for your message). Once your trajectory is loaded in (from command line):
vmd -f trj.dcd prot.psf
go to:
Graphics>Representations>Trajectory
in the field “Draw Multiple Frames” replace “now” with x:y:z where x is the first frame to display (starting from 0), y is the skip step, and z is the last displayed frame. In the case of a trajectory of 50 frames I would write something like:
1:1:50
That’s it! Your trajectory is overlayed.
Wordom: a program for efficient analysis of molecular dynamics simulations
Posted: August 27, 2007 Filed under: geek, papers Leave a comment »Seeber M, Cecchini M, Rao F, Settanni G, and Caflisch A. Bioinf. (2007) doi:10.1093/bioinformatics/btm378
Uncovering the topology of configuration space networks
Posted: August 26, 2007 Filed under: analytic_results, CSN, networks, papers, protein_folding Leave a comment »Gfeller D, De Los Rios P, Morton de Lachapelle D, Caldarelli G, and Rao F. Phys. Rev. E (2007) 76:026113
Complex network analysis of free-energy landscapes
Posted: February 6, 2007 Filed under: analytic_results, clusterization, CSN, networks, papers, protein_folding, transition_state Leave a comment »Gfeller D, De Los Rios P, Caflisch A, Rao F. PNAS (2007) 104:1817-22
[view it in pubmed][pdf][suppmat]
Estimation of folding probabilities and phi values from molecular dynamics simulations of reversible Peptide folding
Posted: January 1, 2007 Filed under: book_chapter, papers, protein_folding, transition_state, Uncategorized Leave a comment »Rao F, Settanni G, Caflisch A. In Y. Bai and R. Nussinov, editors, Methods Mol Biol. (2007) 350:225-49
[view it in pubmed][pdf]
Local modularity measure for network clusterizations
Posted: November 7, 2005 Filed under: clusterization, networks, papers Leave a comment »Muff S, Rao F, Caflisch A. Phys Rev E (2005) 72:056107
[view it inpubmed][pdf]
Estimation of protein folding probability from equilibrium simulations
Posted: May 8, 2005 Filed under: papers, protein_folding, transition_state Leave a comment »Rao F, Settanni G, Guarnera E, Caflisch A. J Chem Phys (2005) 122:184901
[view it in pubmed][pdf][suppmat]
Φ-Value analysis by molecular dynamics simulations of reversible folding
Posted: January 18, 2005 Filed under: papers, protein_folding, transition_state Leave a comment »G Settanni, F Rao, A Caflisch. PNAS (2005) 102:628–633
[view it in pubmed][pdf][suppmat]
Replica exchange molecular dynamics simulations of amyloid peptide aggregation
Posted: December 1, 2004 Filed under: aggregation, papers, replica_exchange 4 Comments »Cecchini M, Rao F, Seeber M, Caflisch A. J Chem Phys (2004) 121:10748-56
[view it in pubmed][pdf]
The protein folding network
Posted: September 3, 2004 Filed under: CSN, networks, papers, protein_folding 1 Comment »F Rao, A Caflisch – J. Mol. Biol (2004), 342: 299–306
[view it in pubmed][pdf][suppmat]
Frequency-domain study of alpha-relaxation in the Random Orthogonal Model
Posted: January 1, 2004 Filed under: papers, physics Leave a comment »Rao F, Crisanti A and Ritort F. Phil Mag (2004) 84:1389
[view it]
Replica exchange molecular dynamics simulations of reversible folding
Posted: August 16, 2003 Filed under: papers, protein_folding, replica_exchange Leave a comment »F. Rao and A. Caflisch. (2003) J Chem Phys 119:4035-4042
[pdf]
