Mac OS X Applications Q-S
QuantumBio :- QuantumMechanics
The pressure is on: optimize lead compounds faster and at less cost. Whether you are discovering leads through Virtual Screening (VS), High Through Screening (HTS) or combining VS & HTS, Lead Optimization involves complex, and expensive multi-step process of refining the chemical structure of a compound to improve its drug characteristics with the goal of producing a preclinical drug candidate. Researchers focus on a number of considerations in optimizing a drug candidate, some of those characteristics are Potency, Toxicity, Metabolism and Formulation. QuantumBio offers the following lead optimization capabilities for your drug discovery investment:
- Use QM based Scoring Function to predict protein-ligand binding affinities on a daily basis.
- Build computational expensive QM descriptors for QSAR & ADME/Tox Models.
- Study protein-ligand complexes containing metals.
- Predict ligand-induced NMR (Nuclear Magnetic Resonance) Chemical Shift Perturbation on protein.
- Study large biomolecules of 500 or 15,000 atoms with QM.
- Understand the Pair-Wise Energy Decomposition of protein-ligand complex interaction.
- Improve QSAR (Quantitative Structure-Activity Relationships) understanding with Quantum Chemistry Molecular Field Analysis (MFA).
- Leverage the accuracy and speed of divide & conquer linear-scaling QM.
Q-Chem :- Ab Initio
Q-Chem is a comprehensive ab initio quantum chemistry package. Its capabilities range from the highest performance DFT/HF calculations to high level post-HF correlation methods. Q-Chem tackles a wide range of problems in commercial, academic and government laboratories, including:
Molecular Structures Chemical Reactions Molecular Vibrations Electronic Spectra NMR Spectra Solvation Effects
- Fast DFT calculations with accurate linear scaling algorithms
- A wide range of post-HF correlation methods that are efficient and unique
- Quantum calculations extended with QM/MM and molecular dynamics
QMForge:- program used to analyze the results of quantum chemistry (DFT) calculations.
QMForge is a program used to analyze the results of quantum chemistry (DFT) calculations. Gaussian 98/03/09, ADF, GAMESS (US), GAMESS (UK), PC-GAMESS, Jaguar, and ORCA files are supported. The following analyses are available:
Mulliken Population Analysis (MPA) C-squared Population Analysis (CSPA) Löwdin Population Analysis (LPA) Overlap Population Analysis (OPA) Mayer's Bond Orders Charge Decomposition Analysis (CDA) Fragment Analysis
QMForge has been created using the following dependencies:
- The Python scripting language (2.7.5),
- The Qt4 toolkit and its Python extensions PyQt4,
- NumPy (1.7.1),
- PyQwt (5.2.0), and
- The cclib computational library (v1.2b).
- OpenBabel and its Python bindings
- The Python Imaging Library (PIL)
QMForge has only been extensively tested on Mac OS X Snow Leopard and Mavericks
Tenderholt, Adam L. QMForge, Version 2.3.2, http://qmforge.sourceforge.net. Tenderholt, Adam L. "QMForge: A Program to Analyze Quantum Chemistry Calculations", Version 2.3.2, http://qmforge.sourceforge.net.
QUACPAC:- pKa and tautomer enumeration
QUACPAC provides pKa and tautomer enumeration in order to get correct protonation states. It also offers multiple partial charge models (including MMFF94 , AM1-BCC , and AMBER ) that cover a range of speed and quality in order to allow appropriate charging for every end use. QUACPAC's approach to tautomeric enumeration is to provide multiple tautomeric states rather than one "correct" tautomer. Subsequent downstream processes are then used to identify the appropriate tautomeric form.
Quantum Expresso:- Electronic structure calculations
QuteMol:- Molecule visualiser
QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins. * Real Time Ambient Occlusion * Depth Aware Silhouette Enhancement * Ball and Sticks, Space-Fill and Liquorice visualization modes * High resolution antialiased snapshots for creating publication quality renderings * Automatic generation of animated gifs of rotating molecules for web pages animations * Real-time rendering of large molecules and protein (>100k atoms) * Standard PDB input
Rasmol :-Molecule viewer
RASMOL UCB enhanced :- Molecule Viewer
How has MultiCHEM enhanced the program?
- Multiple Molecules: Up to five molecules can be viewed in the same canvas window.
- Molecules Window: New window displays molecules currently loaded, allows selection of active molecule.
- Toolbar: Commonly used commands are easily accessed from a graphical toolbar.
- World Rotation: Individual molecules can be rotated about their individual centers of gravity, or the entire world can be rotated around the center of the screen.
- Bond Rotation: Part of a molecule can be rotated about a bond.
- Distance Command: Find distance between two atoms
- Angle Command: Find angle between 3 atoms
- Dihedral Angle Command: Find dihedral angle of 4 atoms
- Distance/Angle Labels: Distances, angles and dihedral angles are labeled directly on the molecule.
Raster 3D :- Molecule images
RAVE:-single and multiple crystal real-space electron-density averaging
Reaxys:- Chemical Reaction and substance searching
- ChemAxon's Marvin Sketch
- Symyx ISIS/Draw (version 2.5 or higher; connection software included in Reaxys Structure Editor plugin)
- Symyx Draw (version 3.0 or higher; connection software included in Reaxys Structure Editor plugin)
- CrossFire Structure Editor (version 7.0 or higher; connection software included in Reaxys Structure Editor plugin)
- CambridgeSoft ChemDraw (version 11 or higher; connection software NOT included in plugin.)
- InfoChem ICEdit (version 1.8 or higher; connection software NOT included in plugin. )
RED:- RESP ESP charge Derive
RefMac:- Macromolecular Refinement Program
The REFMAC program can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where "missing data" have been restored.
RegExRX:- A complete regular expression development tool
I don’t use regular expressions often enough to become an expert but I do use them often enough to know how valuable they are. I always seem to spend more time than I’d like sorting out the regular expression and I often feel that I’ve done something similar before.
I came across an application that I think will make my life a lots easier, RegExRX is a regular expression development tool.
A complete regular expression development tool meant for novices and professionals alike, this editor has many features designed to help in the development and storage of regular expressions. Based on the PCRE library, RegExRX will allow a user to craft patterns that are compatible with most regular expression flavors and will let them easily copy those patterns to other languages like Objective-C, Perl, Ruby, PHP and Xojo.
ome features include:
- Search and Replace modes.
- Color-coded tokens in both the "search" and "replace" patterns.
- Live matching against source text. Live replace too, where applicable.
- Insert menus with almost every acceptable token and a description of what they do, including constructs for various groupings, conditionals, lookarounds, and POSIX expressions.
- A "Match List" that shows all matches, with subexpressions and group names, and represents invisible characters like a space or return with their token equivalents ("\s" or "\r").
- A Templates menu for oft-used patterns. Save As Template from the File menu, or download free samples from our website directly into the Templates folder.
- Export the Match List to a text file, Excel, or FileMaker Pro XML.
- Save the Replaced Text to a text file.
- Stats on both the source text and replaced text so you can tell exactly where you are and what characters are represented at all times. Helps avoid errors caused by invisible characters.
- Linked scrolling among the source text, the replaced text and the Match List.
- Support for Unicode tokens, verbs, and subroutines.
- Save regular expressions in documents for reuse.
- Open as many windows as desired.
- Multiple levels of undo and redo.
- Link your sample source text to a file for easy reloading.
- Support for free-spacing mode.
- Full Unicode support, including a chart of all Unicode characters.
- A fluid interface that lets you resize each panel freely.
RDKit:- Cheminformatics toolkit
Ribbons :- Molecule viewer
RMG (Real Space MultiGrid) is an open source density functional theory electronic structure code distributed under the GNU General Public License. It solves Kohn-Sham equations directly on a 3D real space grid without using basis set functions. RMG is highly scalable; it has been run on supercomputers with thousands of CPU cores. https://en.wikipedia.org/wiki/RMG_(program))
rNMR:- An add-on for R
rNMR is an add-on for R.
rNMR is an open source software package for visualizing and interpreting one and two dimensional NMR data. In contrast to most existing 2D NMR software, rNMR is specifically designed for high-throughput assignment and quantification of small molecules. As a result, rNMR supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks.
I’ve added it to the spectroscopy page.
ROCS :- Molecular shape comparison
SAMSON:- a novel software platform for computational nanoscience
SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON’s generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means “Software for Adaptive Modeling and Simulation Of Nanosystems”.
SARchitect :- Explore structure activity relationships
Sarchitect has a wide range of graphical visualizations to enable visual analysis. The viewing options include: 2D/3D Chemical Structure viewer, 2D/3D Scatter Plots, Profile Plot, Heat Maps, Box-whisker Plots, Histograms, Matrix Plots, Bar Charts and Chemical Space views.
All views in Sarchitect are dynamically linked selections in one view get highlighted all other open views.
Similarly, a range of powerful algorithms enable launching algorithmic inquiry.
For feature selection:
- Statistical Tests & Correlation
- Forward/Backward Selection
- GA Wrappers
- Random Walk
Scaffold Hunter :- Explore structure activity
Scaffold Hunter is a JAVA-based software tool for the analysis of structure-related biochemical data. It enables generation of and navigation in a scaffold tree hierarchy annotated with various data.
SciFinder :- Scientific literature search
Scilab :- Numerical analysis
SciPy :- Numerical analysis
Screening Assistant 2:- Chemical Database analysis
Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering.
A recent publication describes it in detail. Mining Chemical Libraries with "Screening Assistant 2, Vincent Le Guilloux, Alban Arrault, Lionel Colliandre, Stéphane Bourg, Philippe Vayer and Luc Morin-Allory. DOI
SDF2XYZ2SDF:- Cheminformatics link to TINKER
The sdf2xyz2sdf package consists of two programs:
sdf2xyz2sdf depends on OpenBabel for MMFF atom type and charge assignment. Since input to sdf2tinkerxyz is entered through standard input, and output from tinkerxyz2sdf is printed on standard output, it is possible to pipe output from OpenBabel into sdf2tinkerxyz, or to pipe tinkerxyz2sdf output into OpenBabel, so that virtually any format conversion from/to TINKER XYZ may be accomplished.
Interestingly, also ionic heteroaromatic rings which could not be assigned proper charges by the original TINKER-MMFF code are correctly accounted for by sdf2xyz2sdf.
Reference J Mol Model
Sdfchecker:- inspection and manipulation program for SDFiles (.sdf).
Sdfchecker is a free inspection and manipulation program for SDFiles (.sdf). Summary of functions: - Indicate number of structure records - Indicate number of blank structure records - Display list of Data Field names - Remove blank structure records - Split large files into smaller multiple files, a single random sized file, or containing a specified range of records - Convert into individual MOL files - Inspect for duplicate Data Field names within each record
SeeSAR:- tool for interactive, visual compound prioritization and design
SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximize the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR.
ShaEP :- Molecular overlayer
Mikko J. Vainio, J. Santeri Puranen and Mark S. Johnson (2009) ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential. J. Chem. Inf. Model. Article ASAP.
Shape-it:- shape-based alignment tool
Shape-it™ is a shape-based alignment tool by representing molecules as a set of atomic Gaussians. The software is based on the method described by Grant and Pickup (J. Phys. Chem. 1995, 99, 3503).
Siesta :-ab initio simulation of solids
SIMPSON:- General Simulation Program for Solid-State NMR
SIMREF:-structure refinement program for the simultaneous evaluation of several powder diffraction data sets
Situs:- modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering
SIR2008:- Direct Method program for the resolution and refinement of crystal structures using single crystal data
SketchEl:- Molecular drawing
SMARTCyp:- Predict CYP mediated metabolism
The new version includes a specific CYP2D6 model and improved reactivity for benzothiophene sulfurs.
A paper describing the CYP2D6 model has also been published in ACS Medicinal Chemistry Letters.
Smell-o-mints :- Periodic table
smi23D:- Convert SMILES to 3D structures
The source code for the programs can be obtained from the CICC-Grid Sourceforge SVN repository and binary builds are available for Intel Mac OS X.
Smina:- Docking and scoring
Smina is a fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.
SMSD: Calculate MCS
SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will help us to find similarity/distance between two molecules. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure).
SnB:- Crystal structure determination
Solutions:- iPhone app for calculating concs of buffers
needed before making chemical solutions.
Solver:- Linear programming for Excel
SOMA:- Web-based molecular modelling
Open Source Molecular Modelling Workflow Environment
SOMA2 is a versatile modelling environment for computational drug discovery and molecular modelling. SOMA2 is operated through WWW-browser. The SOMA2 environment offers a full scale modelling environment from inputting molecular data to visualisation and analysis of the results.
Kinnunen, T., Nyrönen, T., Lehtovuori, P., SOMA2 - Open Source Framework for Molecular Modelling Workflows, Chemistry Central Journal, 2(Suppl 1):P4 (2008)
Sparky :-NMR analysis
Spartan :- Molecular modelling
SPROUT:- de novo design tool
The system is modularised and offers automatic methods for solving a number of problems in drug design. The user maintains control and is able to guide and modify each module for maximum versatility.
The individual modules serve the following functions:
▪ Binding pocket identification in the solvent accessible surface of the protein complex
▪ Identification of favourable hydrogen bonding, metal bonding and hydrophobic regions or target sites within the binding pocket
▪ Docking of functional groups to target sites to form starting fragments for structure generation
▪ Fragment joining to build skeletons from the starting groups by satisfying the steric constraints of the binding pocket
▪ Scoring and sorting the solutions on binding affinity, complexity anaysis to estimate synthetic feasbility, searching for substructures
SQLGrinder :- SQL tool
Stardrop:- Platform for supporting drug discovery
ADME QSAR models – predict a full range of ADME properties
P450 metabolism models – guide your chemistry to resolve metabolic liabilities
'Chemical space' visualisation and compound selection tools – explore the full chemical space of your chemistry
‘Probabilistic’ scoring – estimate each compound's likelihood of success using data on many properties simultaneously
Glowing Molecule visualisation - Interactively redesign compounds
Auto-Modeler - develop and deploy models of your own data
Strip-it:- Extract molecular scaffolds
Strip-it™ is a tool to extract molecular scaffolds according predefined rules. These rules are based on the definitions of scaffolds as described by Murcko (J. Med. Chem. 1996, 39, 2887), Pollock (J. Chem. Inf. Model. 2008, 48, 1304) and Schuffenhauer (J. Chem. Inf. Model. 2007, 47, 47).
Sugarmagnolia :- Carbohydrate Mass Spec
SugarMagnolia, a freeware program to use as an aid when interpreting mass spectrometric data from carbohydrates. It can calulate the molecular weight of carbohydrates, calculate fragment ions (B-, C-, Y-, and Z-type ions), modify the complete molecule or, modify individual residues, save and print sequences.
Sweet J :- Calculator for the Karplus Equation
Swiss-Pdb Viewer :-Molecule viewer
SYBYL-X:- Molecular modelling
- SYBYL-X from Tripos is a high end molecular modeling package that provides tools for almost every aspect of molecular modeling.
- Small molecule and macromolecule modelling
- 3D QSAR: use the power of industry leading CoMFA in a new way to generate novel ideas for R-groups — predict the level of biological activity or potency based on structure-activity data, not just yes/no activity predictions
- Ligand-based virtual screening: search millions of compounds overnight — don’t miss hits because you only screened subsetted portions of your database
- Cheminformatics: produce highly focused queries that avoid false positives using rich set of 3D queries; on-the- fly conformational searching means you only store a single conformation of your molecules, keeping database size small and very transportable
- Docking: custom tailor and fine-tune docking to a particular receptor site using information like SAR or known poses to improve rank ordering of ligands
SZYBKI:- optimizes molecular structures with the Merck Molecular Force Field
SZYBKI optimizes molecular structures with the Merck Molecular Force Field, either with or without solvent effect, to yield quality 3D molecular structures for use as input to other programs. Since the chemistry of molecular interactions is a matter of shape and electrostatics, it is impossible to consider either without reasonable 3D molecular structures. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.
SZMAP:- Water mapping in protein
SZMAP uses semi-continuum Poisson-Boltzmann electrostatics to map variations in solvent properties in a protein binding site. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding. The newly released tool GAMEPLAN, suggests ways to modify ligand chemistry based on this understanding of water structure in the immediate environment of the ligand.