Blog Archives

Contact Module in Maestro - contact cutoff ratio

11/30/2012

In Maestro when visualizing a structure file, you can select Tools -> Measurements -> Contacts panel in order to see Good contacts and Bad&Ugly contacts. When contacts are displayed, good contacts are green by default, bad ones are orange, and ugly ones are red. These criteria whether a contact is defined as good, bad or ugly are based on the following formula:

C = D12 / ( R1 + R2 )

where D12 is the distance between atomic centers 1 and 2, and R1 and R2 are the radii of atomic centers 1 and 2. C is defined as the "contact cutoff ratio" in Maestro and has default values of 0.85 for "Bad" contacts and 0.70 for "Ugly" contacts. C must be monotonically increasing for each of the contact types, that is C(ugly) < C(bad) < C(good). These three values then provide 4 ranges. Distances greater than C(good) are not marked, less than C(good) but greater than C(bad) are marked as "good", etc.

This answer was provided by the Schrodinger help team.

Zoe

1 Comment

libstdc++.so.6: version `GLIBCXX_3.4.11' not found

11/23/2012

1 Comment

While trying to use some of Desmond tools I got the following error:

/opt/desmond2012/maestro-v93023/lib/Linux-x86_64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib/pymodules/python2.7/matplotlib/ft2font.so)

The solution is to instal the GNU C compiler and GNU C++ compiler for x86_64.
To install the gcc and g++ compilers, you will need the build-essential package. This will also install GNU make.
build-essential contains a list of packages which are essential for building Ubuntu packages including gcc compiler, make and other required tools.

$ sudo apt-get update
$ sudo apt-get upgrade
$ sudo apt-get install build-essential
$ gcc -v
$ make -v

Then,
$ cd /opt/desmond2012/maestro-v93023/lib/Linux-x86_64
$ sudo mv libgcc_s.so.1 libgcc_s.so.1.back
$ sudo ln -s /lib/libgcc_s.so.1 libgcc_s.so.1
$ sudo rm libstdc++.so.6 (this was already a symbolic link)

and finally create a symbolic link
$ sudo ln -s /usr/lib/gcc/x86_64-linux-gnu/4.6.1/libstdc++.so libstdc++.so.6

Hope that helps!
Evi

1 Comment

Managing Projects Effectively

11/21/2012

0 Comments

The ACS Leadership Development System™ is now offering online training. These convenient, self-paced online courses offer top-quality information on your schedule; check out this week's featured course:

Managing Projects Effectively: Successful projects don’t happen on their own, they require a skilled leader to set clear goals and ensure they are met. Managing Projects Effectively is a self-paced online course that will help you improve your ability to lead projects to completion – on time, within budget, optimizing your resources, and achieving your goals. As a leader, you will gain practical skills that you can immediately apply to your professional and volunteer endeavors. Course fee: ACS Members, $25; non-members, $50

Visit the ACS Leadership Development System™ to learn more about this and other leadership development courses, or register online.

Zoe

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Voipbuster

11/14/2012

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Voipbuster is a Voice over IP software that offers services such as:

a) Phone2Phone:
You can enter your phone number and then the number you want to call. Voipbuster will call your number first, and then dial the number you want to call and connect this to your landline.

b) If you don't want to be charged by Voipbuster for the call to your landline, you can dial the VoipBuster local number (for Greece it is: +302111980036) and then dial the number you wish. Voipbuster buster offers free calls to many countries (see below).

c) If you don't want to install our Voipbuster software, you can set up a Voipbuster call directly, Voipbuster offers an in-browser solution for calling: Phone-2-Phone

d) You can also call all your online friends (pc-to-pc calls) as long as you like, for free.

e) You can also send SMS texts for a low cost.

Free Countries (landline)
Andorra
Australia
Austria
Belgium
Canada
Cyprus
Czech republic
Denmark
Estonia
Finland
France
Guam
Hong kong mobile
Hong kong
Hungary
Iceland
Ireland
Italy
Japan
Luxembourg
Malaysia
Netherlands
New zealand
Norway
Portugal
Puerto rico mobile
Puerto rico
Russian federation [moscow]
Singapore
South korea
Spain
Switzerland
Taiwan
United states mobile
United states

Zoe

0 Comments

Protein and molecule rendering in Matlab

11/7/2012

2 Comments

In this link you can find details about rendering proteins or molecules with Matlab.
Evi

2 Comments

Analysis of MD simulations using GROMACS tools

11/7/2012

5 Comments

I just came across this presentation which very nicely summarises the most important analysis tools for proteins available in Gromacs: Definitely worth reading and very good as a reference for experienced gromacs users.

Analysis tools that you can find in the presentation include:
- Looking at your trajectory
- Groups in analysis
- Root mean square deviations and fluctuations
- Radius of gyration and distances
- Hydrogen bonds
- Secondary structure analysis
- Free energy surfaces
- Principal component analysis: using Cartesian coordinates or dihedral angles
- Clustering

Evi

5 Comments

CycloPs: generating virtual libraries of peptides

11/6/2012

1 Comment

CycloPs is a software for generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids.

Here is the abstract from Pubmed:

We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-dimensional SMILES and three-dimensional SDF formats, suitable for virtual screening. The stand-alone software is capable of filtering the virtual libraries using empirical measurements, including peptide synthesizability by standard peptide synthesis techniques, stability, and the druglike properties of the peptide. The software and accompanying Web interface is designed to enable the rapid generation of large, structurally diverse, synthesizable virtual libraries of constrained peptides quickly and conveniently, for use in virtual screening experiments. The stand-alone software, and the Web interface for evaluating these empirical properties of a single peptide, are available at http://bioware.ucd.ie .

Zoe

1 Comment

Peptide-protein docking

11/5/2012

3 Comments

Some programs that I have found to perform peptide docking:

1) Rosetta FlexPepDock is a high-resolution peptide docking (refinement) protocol, implemented within the Rosetta framework. The input for this server is a PDB file of a complex between a protein receptor (first chain) and an estimated conformation for a peptide (second chain). FlexPepDock was shown to be able to accurately refine the peptide structure starting from up to 5.5A RMSD of the native conformation, allowing full flexibility to the peptide and side-chain flexibility to the receptor.

2) Autodock. Autodock itselft as well as PSO@Autodock can be used to dock small peptides on a protein.

3) eHiTS. See also
http://www3.interscience.wiley.com/journal/121657999/abstract?CRETRY=1&SRETRY=0

4) ICM-Dock. Flexible peptide-receptor docking.

A useful link listing many of the docking programs and their capabilities can be found here.
If you happen to know of more programs please let us know!

Zoe

3 Comments

Structural Analysis and Verification Server

11/4/2012

2 Comments

The Structural Analysis and Verification Server performs the following functions:

1) Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry. [Reference]

2) Does extensive checking of many sterochemical parameters of the residues in the model. [Reference]

3) Analyzes the statistics of non-bonded interactions between different atom types and plots the value of the error function versus position of a 9-residue sliding window, calculated by a comparison with statistics from highly refined structures. [Reference]

4) Determines the compatibility of an atomic model (3D) with its own amino acid sequence (1D) by assigned a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures. [Reference]

5) Calculates the volumes of atoms in macromolecules using an algorithm which treats the atoms like hard spheres and calculates a statistical Z-score deviation for the model from highly resolved (2.0 Å or better) and refined (R-factor of 0.2 or better) PDB-deposited structures. [Reference]

Zoe

2 Comments

Contact Module in Maestro - contact cutoff ratio

libstdc++.so.6: version `GLIBCXX_3.4.11' not found

Managing Projects Effectively

Voipbuster

Protein and molecule rendering in Matlab

Analysis of MD simulations using GROMACS tools

CycloPs: generating virtual libraries of peptides

Peptide-protein docking

Structural Analysis and Verification Server

Alexis, Michalis, Danai, Panos, Sotiris, Nastazia, Vassilis, Zoe

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