biophysics.cs.vt.edu

H++ (web-based computational prediction of protonation states and pK of ionizable groups in macromolecules)

H is an automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools for analysis of electrostatic-related molecular properties. Why H. If this is your first time using H , please read the FAQ carefully. H in more detail. Citations. The accuracy tabl...

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H++ (web-based computational prediction of protonation states and pK of ionizable groups in macromolecules) | biophysics.cs.vt.edu Reviews

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H is an automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools for analysis of electrostatic-related molecular properties. Why H. If this is your first time using H , please read the FAQ carefully. H in more detail. Citations. The accuracy tabl...

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1 pK

2 protonation

3 prediction

4 computation

5 web

6 web-based

7 automatic

8 biomolecule

9 protein

10 ligand

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H++ (web-based computational prediction of protonation states and pK of ionizable groups in macromolecules) | biophysics.cs.vt.edu Reviews

https://biophysics.cs.vt.edu

H is an automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools for analysis of electrostatic-related molecular properties. Why H. If this is your first time using H , please read the FAQ carefully. H in more detail. Citations. The accuracy tabl...

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biophysics.cs.vt.edu

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H++ (web-based computational prediction of protonation states and pK of ionizable groups in macromolecules)

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H++ (web-based computational prediction of protonation states and pK of ionizable groups in macromolecules)

http://biophysics.cs.vt.edu/faq.php

Q: Who can use H? A: Unlimited free access to this site is restricted to non-profit use (including academic and educational). If you intend to use it for any other purpose, please contact the development team to obtain proper license. (Regardless of the purpose, you can test run the site for up to three weeks. But please avoid submitting very large structures. ). Q: Do I need to log in? A: No, it is not necessary to log in, you can process (small) structures anonymously. Q: Why would I want to register?

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H++ (web-based computational prediction of protonation states and pK of ionizable groups in macromolecules)

http://biophysics.cs.vt.edu/index.php

H is an automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools for analysis of electrostatic-related molecular properties. Why H. If this is your first time using H , please read the FAQ carefully. H in more detail. Citations. The accuracy tabl...

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H++ (web-based computational prediction of protonation states and pK of ionizable groups in macromolecules)

http://biophysics.cs.vt.edu/credits.php

Ramu Anandakrishnan ( ramu@vt.edu. Lead developer. Responsible for adding the ligand and nucleic acid capabilities and for general maintenance. Boris Aguilar ( baguilar@cs.vt.edu. Software developer. Responsible for many aspects of the system development and maintenance. Original (circa 2004-2005 ) team that built and launched H 1.0:. John Gordon ( jogordo3@vt.edu. Lead developer and supervisor. Responsible for most aspects of the system development and maintenance. Jonathan Myers ( jonmyers@vt.edu.

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H++ (web-based computational prediction of protonation states and pK of ionizable groups in macromolecules)

http://biophysics.cs.vt.edu/H++

H is an automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools for analysis of electrostatic-related molecular properties. Why H. If this is your first time using H , please read the FAQ carefully. H in more detail. Citations. The accuracy tabl...

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people.cs.vt.edu

Dr. Alexey Onufriev

http://people.cs.vt.edu/~onufriev/software.php

H : Automated prediction of pK and protonation states in macromolecules. 12CG Coarse-grained Molecular Dynamics of the DNA. This is a set of programs to perform coarse-grained MD simulations and calculations of the DNA heat conductivity described in Alexander V. Savin, Mikhail A. Mazo, Irina P. Kikot, Leonid I. Manevitch, and Alexey V. Onufriev. ` Heat conductivity of the DNA double helix", Phys. Rev. B 83, 245406 (2011). PATHFINDER (beta 0.1): analysis of voids in macromolecules. Jory Z. Ruscio, Dee...

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http://pengfei-li.weebly.com/tutorials.html

Welcome to Pengfei (Jimmy) Li's website! Welcome to Pengfei (Jimmy) Li's Webpage. Material system modeling tutorial. Could be found in the webpage of AMBER tutorial A27. Metal ion modeling tutorial. I have written an AMBER metal ion modeling tutorial. With my advisor Prof. Kennie Merz. It contains instructions of ion modeling for different models. Please click on the following link if you are interested: Metal Ion Modeling Tutorial. How leap program works in amber. I Terminology used in this tutorial.

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H++ (web-based computational prediction of protonation states and pK of ionizable groups in macromolecules)

H is an automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools for analysis of electrostatic-related molecular properties. Why H. If this is your first time using H , please read the FAQ carefully. H in more detail. Citations. The accuracy tabl...

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