NBOView from THEORETICAL CHEMISTRY INSTITUTE - UNIVERSITY OF WISCONSIN

Erin R. Johnson, Shahar Keinan, Paula Mori-Sanchez, Julia Contreras-Garcia, Aron J. Cohen, and Weitao Yang, J. Am. Chem. Soc. 2010, 132, pp 6498-6506. J. Contreras-Garcia, E. R. Johnson, S. Keinan, R. Chaudret, J-P. Piquemal, D. N. Beratan, and W. Yang. J. Chem. Theory Comput. 2011, 7, pp 625-632.

Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is installed on the system while Open3DALIGN is being operated interactively, the setup of alignments can be followed in real time on PyMOL's viewport.

Open3DGRID is an open-source software aimed at high-throughput generation of molecular interaction fields (MIFs). Open3DGRID can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID and CoMFA/CoMSIA fields (exported from SYBYL with the aid of a small SPL script).

open enventory is an integrated laboratory journal with a literature database and inventory program. It is a web application (Internet Explorer 7, Firefox 3.5, Opera 9.52, Apple Safari, Google Chrome) and therefore platform independent (find technical information here). The integration makes physical data and safety informationen from the inventory automatically accessible in the laboratory journal. The automatic acquisition of freely accessible data from online databases makes manual data acquisition and catalogue searches obsolete. Accessing the online catalogues also allows price surveys with a mouseclick.

ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.

Parallel Quantum Solutions We estimate that well over 80% of CPU cycles spent in ab initio computations are used in optimizing geometries at the SCF or DFT levels,and in computing molecular properties, such as vibrational frequencies and NMR chemical shifts. Such calculations are extremely well suited for parallel implementation. Shifting them to an inexpensive and fast parallel machine can free up expensive workstations for more demanding calculations.

• Read NetCDF GC/MS files
• Identify peaks in chromatograms
• Identify compounds associated with peaks
• Make a summary of all your analyses

Python-based Hierarchical ENvironment for Integrated Xtallography

PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods

On Macintosh, either G5 PPC or Intel machines are supported, and require at least OS 10.4.11 (10.6.7 for the 64-bit version). Support for G5 systems may be dropped in the future. Additional information on Mac platform support is available here.

POSIT is primarily based on the assumption that similar ligands bind similarly. Unlike most docking protocols, POSIT requires the presence of a known bound ligand. The bound ligand is used to impart docking constraints when placing and optimizing the geometry of the molecule being docked.

ProDy is a free and open-source Python package for protein structural dynamics analysis. It is designed as a flexible and responsive API suitable for interactive usage and application development.

Structure analysis

ProDy has fast and flexible PDB and DCD file parsers, and powerful and customizable atom selections for contact identification, structure comparisons, and rapid implementation of new methods.

Dynamics analysis

• Principal component analysis can be performed for ◦ heterogeneous X-ray structures (missing residues, mutations) ◦ mixed structural datasets from Blast search ◦ NMR models and MD snapshots (essential dynamics analysis)
• Normal mode analysis can be performed using ◦ Anisotropic network model (ANM) ◦ Gaussian network model (GNM) ◦ ANM/GNM with distance and property dependent force constants

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments 2011 Bioinformatics 27(11):1575-1577 DOI

• Arbitrarily high angular momentum levels in integrals and derivative integrals. (Up to m-type functions have been tested.)
• Coupled cluster methods including CC2, CCSD, CCSD(T), and CC3 with RHF, ROHF, UHF, and Brueckner orbitals.
• Determinant-based CI including CASSCF, RAS-CI, and Full CI.
• Multithreaded integral-direct SCF, MP2, and MP2-R12.
• Excited state methods: CIS, CIS(D), RPA, EOM-CCSD, and CC3.
• Analytic energy gradients for CCSD with RHF, ROHF, and UHF orbitals.
• Coupled cluster linear response methods for static and dynamic polarizabilities and optical rotation.
• Diagonal Born-Oppenheimer correction (DBOC) for RHF, ROHF, UHF, and CI wave functions.

inner energy, enthalpy, Helmholtz free energy, Gibbs free energy, entropy, heat capacity at constant V and P, ideal heat capacity at constant P, speed of sound, isobaric expansion coefficient, relative pressure coefficient, isothermal compressibility, Joule Thompson coefficient, isentropic temperature-pressure coefficient, isothermal throttling coefficient, isothermal stress coefficient, second virial and third coefficient, fugacity and fugacity coefficient, compressibility factor.

The program allows the calculation of the thermodynamic properties at arbitrary temperature and density or pressure conditions (List), tables with even spaced increments of temperature and density/volume (Table), or properties at the vapor saturation curve (Saturation). All these results are listed in Report tab which can be printed. The Plot tab allows the graphical representation of the thermodynamic properties for various conditions and includes the calculation of isopleths. These plots can be also printed. The Unit tab allows the user to choose the appropriate units for the individual thermodynamic properties.

By default the thermodynamic values for the inner energy, the enthalpy, the entropy, the Helmholtz free energy, and the Gibbs free energy are calculated as reported by the respective EOS. If required, the values for these properties can be corrected for an ideal gas with H = 0 and S = 0 at respective reference conditions (typically 298.15 K and 0.1 MPa). The reference conditions, however, can be chosen by the user.

Lists, normal and saturation tables, and plots can be also exported. The Help menu provides all the references for the respective EOS

PyMOL A 3D molecule viewer, PyMOL is a powerful molecular graphics package for structural biology and other sciences. This interactive system is fully scriptable using the Python computing language, sponsored and supported by users.

The compiled PYMOL binaries are available for paid download with different options for academic, industrial and non-profit.

In addition the source code is available for free download. Not all new features make it to the source code right away, but eventually all features will, usually within a few months

If you would like to enable the use of plugins in PyMol read this tutorial