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APBS and PDB2PQR: electrostatic and solvation properties for complex molecules | apbs-pdb2pqrAPBS and PDB2PQR software
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APBS and PDB2PQR software
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APBS and PDB2PQR: electrostatic and solvation properties for complex molecules | apbs-pdb2pqr | poissonboltzmann.org Reviews
https://poissonboltzmann.org
APBS and PDB2PQR software
poissonboltzmann.org
Support
http://www.poissonboltzmann.org/support/home
This site aims to be a comprehensive guide to APBS and PDB2PQR. Before beginning, please make sure to support the APBS/PDB2PQR team by registering for an account. We have a new combined announcements mailing list for APBS and PDB2PQR. You can view the list archives. And sign up to receive future emails. Archives for our older mailing lists are available at SourceForge ( apbs-announcements. We also maintain support mailing lists for questions and interactive discussion of our software:.
Visualizing Results
http://www.poissonboltzmann.org/docs/visualizing-results
There are several programs available for visualizing your results. If you have used the web server for your calculations, the java jmol plugin may be the easiest method, described directly below. However, if you need more options, there are several external programs, such as pymol. For you to use. The most straightforward way to visualize results is through the web server. If you’ve used the web server to get your structures ready. And calculate the electrostatics. Visualize the electrostatic potential.
News
http://www.poissonboltzmann.org/news
APBS VR Molecular Visualization. PDB2PQR 2.1.1 Released. APBS 1.4.2.1 Released. APBS VR Molecular Visualization. Molecular visualization software packages provide the ability for users to explore the 3D representations molecular structures and properties. Examples of these systems include UnityMol. View of UnityMol form the monitor as it is being used in VR with controllers. PDB2PQR 2.1.1 Released. Dear APBS and PDB2PQR users. There are several improvements and fixes (outlined below) to this release of t...
Welcome
http://www.poissonboltzmann.org/docs/home
This site aims to be a comprehensive guide to APBS and PDB2PQR. What are APBS and PDB2PQR? Adaptive Poisson-Boltzmann Solver) and PDB2PQR. Are software packages designed to help you analyze the solvation properties of small and macro-molecules such as proteins, nucleic acids, and other complex systems. Why APBS and PDB2PQR? Adding a limited number of missing heavy (non-hydrogen) atoms to biomolecular structures. Assigning charge and radius parameters from a variety of force fields. What do I do next?
Examples
http://www.poissonboltzmann.org/examples/home
The following examples will help orient you in APBS/PDB2PQR. Before beginning, please make sure to support the APBS/PDB2PQR team by registering. Best use of examples. Work through the examples in order, which begin with simple processes and end with advanced instances. Assigning Titration States With Propka. Basic PDB File Operations. Running APBS through the PDB2PQR Web Portal. Parallel execution for large problems. Lysozyme pKa example for PDB2PQR 1.9. Potentials of mean force. Basic PDB File Operations.
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Team Bios | Signature Discovery Initiative
https://signatures.pnnl.gov/bios
Pacific Northwest National Laboratory. Luke Gosink - Signature Discovery Initiative Lead. Nathan A. Baker. Nathan A. Baker - Signature Discovery Chief Scientist. George T. Bonheyo. George T. Bonheyo - Signature Discovery Methods. George Bonheyo is a senior research scientist in the Energy and Environment Directorate at Pacific Northwest National Laboratory's Marine Sciences Laboratory in Sequim, Washington. He has over 20 years of experience applying genetic engineering and molecular microbiology to ...
BindUP - Predicting DNA and RNA binding proteins using electrostatic patches
http://bindup.technion.ac.il/overview.html
BindUP holds information for all the protein structures in the RCSB PDB database. And is updated every month. The server is applicable in either single or batch mode and can be applied for testing hundreds of proteins simultaneously in a highly efficient manner. The Patch Finder algorithm. The Patch Finder algorithm automatically assigns surface positive/negative patches by looking for adjacent points on the protein surface that meet a given electrostatic potential cutoff (2 or -2 kT/e). The algorithm fo...
Michael G. Lerner
http://www.mglerner.com/software.php
Michael G. Lerner. Michael G. Lerner and Heather A. Carlson. University of Michigan, Ann Arbor, 2006. The PyMOL-APBS Plugin integrates the PyMOL. Molecular graphics system with APBS. To enable rapid, easy calculation of electrostatic potential surfaces with minimal user intervention. It is included with recent versions of PyMOL and is available directly on the web at the PyMOL wiki. It is one of the most heavily used PyMOL plugin and is responsible for upwards of 80% of all calculations done with APBS.
Anatoly Chernyshev
http://www.achernyshev.com/compchem.html
Last modified: August, 2016. On Amazon Web Services EC2. Possibly could be adapted also for GAMESS US. Disclaimer: this is not a step-by-step guide, rather a bunch of hints of how to avoid many technical issues I personally stumbled upon trying to run Firefly on AWS cluster. For the beginning I strongly advise to look through a couple of excellent videos on StarCluster and its documentation. A general overview of my cluster setup is shown on the picture below:. And saved it as my own custom AMI. The limi...
grupos-jlrt - oldBioinformática
http://grupos-jlrt.wikispaces.com/oldBioinformática
Skip to main content. Get your brand new Wikispaces Classroom now. And do "back to school" in style. Protein2 MAEPRQEFEVMEDHAGTYGLGDRKDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPG SETSDAKSTPTAEDVTAPLVDEGAPGKQAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAG HVTQEPESGKVVQEGFLREPGPPGLSHQLMSGMPGAPLLPEGPREATRQPSGTGPEDTEG GRHAPELLKHQLLGDLHQEGPPLKGAGGKERPGSKEEVDEDRDVDESSPQDSPPSKASPA QDGRPPQTAAREATSIPGFPAEGAIPLPVDFLSKVSTEIPASEPDGPSVGRAKGQDAPLE FTFHVEITPNVQKEQAHSEEHLGRAAFPGAPGEGPEARGPSLGEDTKEADLPEPSEKQPA AAPRGKPVSRVPQLKARMVSKSKDGTGSDDKKA...
McCammon Group
http://deki.mccammon.ucsd.edu/computing
We have recently changed our website. Looking for the previous site? Computational Research in Molecular Chemistry. Available Through the McCammon Group:. Originated in the McCammon Group:.
McCammon Group
http://mccammon.ucsd.edu/computing
We have recently changed our website. Looking for the previous site? Computational Research in Molecular Chemistry. Available Through the McCammon Group:. Originated in the McCammon Group:.
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APBS and PDB2PQR: electrostatic and solvation properties for complex molecules | apbs-pdb2pqr
APBS and PDB2PQR software. View the Project on GitHub. APBS and PDB2PQR: electrostatic and solvation properties for complex molecules. Please register your use. To ensure continued support for the APBS-PDB2PQR software. Read our online documentation. Get started with the web server. Download the software following these instructions. More information about the software. Adding a limited number of missing heavy (non-hydrogen) atoms to biomolecular structures,. This service is intended to facilitate the se...
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