CrystalDock 1.0.0 – Molecular Design and Optimization

CrystalDock 1.0.0

:: DESCRIPTION

CrystalDock is a computer algorithm that aids the computational identification of molecular fragments predicted to bind a receptor pocket of interest. CrystalDock makes direct use of crystallographic and NMR structures from the Protein Data Bank (PDB).

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

CrystalDock

:: MORE INFORMATION

Citation

J Chem Inf Model. 2011 Oct 24;51(10):2573-80. doi: 10.1021/ci200357y. Epub 2011 Oct 5.
CrystalDock: a novel approach to fragment-based drug design.
Durrant JD1, Friedman AJ, McCammon JA.

rnaifold 3.1 – RNA Inverse Folding and Molecular Design

rnaifold 3.1

:: DESCRIPTION

rnaifold is a web server that solves the RNA inverse folding problem, using constraint programming. Given a target RNA secondary structure, as well as optional nucleotide constraints, RNAiFold determines all (or a large number of) RNA sequences, whose minimum free energy structure is the target structure.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 rnaifold

:: MORE INFORMATION

Citation

RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
Garcia-Martin JA, Dotu I, Clote P.
Nucleic Acids Res. 2015 May 27. pii: gkv460.

RNAiFold: A constraint programming algorithm for RNA inverse folding and molecular design
J.A. Garcia-Martin, P. Clote, I. Dotu,
Journal of Bioinformatics and Computational Biology ,DOI: 10.1142/S0219720013500017

Tinker 7.1.3 – Software Tools for Molecular Design

Tinker 7.1.3

:: DESCRIPTION

TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang’s polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases.

::DEVELOPER

Jay Ponder Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

Tinker

:: MORE INFORMATION