Andrew Perry's Library tagged tools →  View Popular

"Protein finder is a gendetector. The program finds genes by performing blastx searches of the input sequence against NR. For each high scoring pair the coverage is calculated. The user can set a threshold for the coverage. Every high scoring pair that meets or exceeds this threshold is reported in an embl file. This embl file can be loaded into artemis together with the DNA sequence."

nbc11.biologie.uni-kl.de/...menu - Preview

protein gene genome genomics orf prediction bioinformatics tools blast web_based

compbio.sookmyung.ac.kr/~qhelix - Preview

protein structure helix modelling software tools

.. yet another protein structural alignment tool added to my list ...

topmatch.services.came.sbg.ac.at - Preview

protein structure alignment tools web_based bioinformatics comparison

www.dmbr.ugent.be/...index.php - Preview

protease web_based bioinformatics tools prediction protein sequence

A Javascript optimizer and compressor, a Javascript library for widgets and DOM manipulation etc, and an HTML templating system for Javascript.

code.google.com/closure - Preview

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toolserver.org/...index.cgi - Preview

tools web_based wiki conversion text

"Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.". You can "sudo apt-get install avogadro" to get it on Ubuntu (although you won't get the latest and greatest version).

avogadro.openmolecules.net/...Main_Page - Preview

ligand drug_design tools software chemistry molecular editor

builder.yaml.de - Preview

webdev css html tools web_based

www.positioniseverything.net/...pagemaker_form.php - Preview

webdev css html tools web_based

A browser-based "console" which provides an interactive Python session, running as part of your Google App Engine app. Allows you to query the datastore of your application while it is running live using Python statements.

con.appspot.com/console - Preview

appengine gae python tools code console webdev

An annotation meta-server. "Annie was born out of the necessity of the Sequence Analysis group to make functional predictions on a wide range of targets arising from in-house projects as well as collaborations. The availability of hundreds of prediction tools makes the effort of functional characterization a tedious tasks with hours spent on sieving through a bewildering range of result formats and outputs."

annie.bii.a-star.edu.sg/...index.jsp - Preview

protein sequence annotation bioinformatics tools web_based prediction

swissmodel.expasy.org/...index.cgi - Preview

protein structure modelling assessment tools web_based bioinformatics

"PASS (Putative Active Sites with Spheres) is a simple computational tool that uses geometry to characterize regions of buried volume in proteins and to identify positions likely to represent binding sites based upon the size, shape, and burial extent of these volumes."

www.ccl.net/...overview.shtml - Preview

protein structure modelling pocket ligand tools software

a web frontend to many bioinformatics & structural bioinformatics tools, including Modeller (if you have a license key).

mobyle.rpbs.univ-paris-diderot.fr/...portal.py - Preview

bioinformatics web_based tools portal modeller

"fpocket is a very fast open source protein pocket (cavity) detection algorithm based on Voronoi tessellation"

fpocket.sourceforge.net - Preview

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"You can choose to monitor any of a broad set of subsystems which currently include buddyinfo, cpu, disk, inodes, infiniband, lustre, memory, network, nfs, processes, quadrics, slabs, sockets and tcp."

collectl.sourceforge.net - Preview

linux sysadmin cluster monitoring top software tools

Prettyprints JSON responses in the browser.

addons.mozilla.org/...10869 - Preview

diigo json firefox webdev tools

"The AD-ENM (Analysis of Dynamics of Elastic Network Model) server performs analysis of macromolecular dynamics based on a highly simplified physical model --- Elastic Network Model (ENM)"

enm.lobos.nih.gov/index.html - Preview

protein md modelling normal_mode tools web_based structure dynamics

Designed for filtering large numbers of protein models based on various properties (solvent accessibility, contact order, RDF shape, secondary structure, etc)

sift.cchmc.org - Preview

protein modelling web_based bioinformatics abinitio tools solvent_accessibility secondary_structure

Adds hydrogens to PDB coordinates, preparation for electrostatics calculations, simulations, docking.

pdb2pqr.sourceforge.net/ - Preview

protein structure docking modelling tools software hydrogens electrostatics