RegExRX

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Download RegExRX - This is a handy tool designed to help you create and manage regular expressions.

QuantumBio :- QuantumMechanics

RegExr is an online tool to learn, build, & test Regular Expressions (RegEx / RegExp). Supports JavaScript & PHP/PCRE RegEx. Results update in real-time as you type. Roll over a match or expression for details. RegExRX (RegExRX.exe). RegExRX is a regular expression development tool. Based on the PCRE library, RegExRX allows you to craft patterns that are compatible with most regular expression flavors; you can also copy these patterns to other languages like Perl, Ruby, PHP, and REALbasic. I personally prefer the RegExRx app, which should work on OSX and Windows and is available either as a shareware version or as a paid app on the Apple App Store. This program includes support for Perl style Regular Expressions which are quite common and are used by some R packages.

ExpressionQuantumBio provides Pharmaceutical and Biotech companies with patent pending fast Quantum Mechanical (QM) solutions for Lead Optimization!
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 the latest version of a modern ab initio electronic structure program, is capable of performing first principles calculations on both the ground and excited states of molecules.
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
Q-Chem provides users with some distinct advantages:
  • 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 OrdersCharge 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)
  • simplejson

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 [1], AM1-BCC [2], and AMBER [3]) 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

Quantum Expresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

Details of the packages is available in the documentation

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 A 3D molecule viewer ported to Mac OS X

RASMOL UCB enhanced :- Molecule Viewer

UCB enhanced RASMOL
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

Raster3D - is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.

RAVE:-single and multiple crystal real-space electron-density averaging

RAVE is a suite of programs for single and multiple domain, single and multiple crystal real-space electron-density averaging. It also contains tools for the detection of secondary structure elements in macromolecular electron-density maps. The package succeeds the previous A suite.

Reaxys:- Chemical Reaction and substance searching

Reaxys is designed for reaction, substance and citation data searching, combined with synthesis planning. Users can search for reactions, methods, compounds, properties and literature queries (authors, journals etc.). Reaxys provides a seamless access to the Scopus abstract and citation database, ScienceDirect online collection of published scientific research—and Beilstein reaction information database.
Reaxys requires Mac OS 10, Safari 3.0 or higher, JRE 5.0 or higher and Javascript and cookies need to be enabled and currently supports the following editors:

  • 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

R.E.D. allows computational biologists involved in AMBER/GAFF, CHARMM, GLYCAM & OPLS force field based biological studies to automatically derive highly effective and reproducible charge values, and to build force field libraries for new molecules and molecular fragments.

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.
  • Copy the find and replace patterns in ready-to-paste code for Objective-C, Perl, PHP, Ruby, AppleScript, JavaScript, 4D, and Xojo.

RDKit:- Cheminformatics toolkit

RDKit: A software suite for cheminformatics, computational chemistry, and predictive modeling written in C++ and Python

Ribbons :- Molecule viewer

Ribbons A popular molecular graphics program.

RMG

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

ROCS is a shape comparison program, based on the idea that molecules have similar shape if their volumes overlay well and any volume mismatch is a measure of dissimilarity. ROCS uses a smooth Gaussian function to represent the molecular volume, so it is possible to routinely minimize to the best global match. ROCS is capable of processing 600-800 comparisons each second, making it is possible to search multi-conformer representations of corporate collections in a day on a single processor to find compounds with similar shape to a lead compound.

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 is a tool for analysing structure activity relationships and ADME/T modeling.


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
For clustering:
  • K-Means
  • Hierarchical
  • SOM
  • Random Walk
Principal Component Analysis

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

SciFinder is now MacOSX native!! it is an easy to use desktop research tool that allows you to explore research topics, browse scientific journals, and stay up to date on today's most recent scientific developments. With SciFinder, no special training is needed. You simply point and click to access more than 19 million abstracts and 35 million substances.

Scilab :- Numerical analysis

Scilab Scilab is a scientific software package for numerical computations in a user-friendly environment

SciPy :- Numerical analysis

ScilPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering. It is also the name of a very popular conference on scientific programming with Python. The core library is NumPy which provides convenient and fast N-dimensional array manipulation. The SciPy library is built to work with NumPy arrays, and provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization. Together, they run on all popular operating systems, are quick to install, and are free of charge. NumPy and SciPy are easy to use, but powerful enough to be depended upon by some of the world's leading scientists and engineers. If you need to manipulate numbers on a computer and display or publish the results, give SciPy a try!

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

sdf2xyz2sdf is an open-source software aimed at converting SDF files into TINKER XYZ files (and viceversa) while performing automatic assignment of MMFF94 atom types, bond types and charges.
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 aspecified 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.

SemiChem :-QSAR

SemiChem report that the semiempirical quantum mechanical program Ampac and advanced, fully featured quantitative structure/activity relationship (QSAR) program Codessa are available for MacOSX

ShaEP :- Molecular overlayer

ShaEP aligns (superimposes) two rigid 3D molecular structure models and computes a similarity index for the overlay. It can be used for the virtual screening of libraries of chemical structures against a known active molecule, or as a preparative step for 3D QSAR methods.
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

Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

SIMPSON:- General Simulation Program for Solid-State NMR

SIMPSON a General Simulation Program for Solid-State NMR. It features multi-pulse 1D/2D experiments on large spin-systems with input-files implemented using a simple scripting language. The program is designed to emulate a NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, rf irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition.

SIMREF:-structure refinement program for the simultaneous evaluation of several powder diffraction data sets

SIMREF a structure refinement program for the simultaneous evaluation of several powder diffraction data sets and multiple phases per data set. With a structural model all calculated diffraction profiles are fitted to the corresponding observed diffraction profile by the method of least squares. This procedure is called Rietveld method (Rietveld, 1969 ). By the simultaneous refinement of several data sets new evaluation techniques are possible

Situs:- modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering

Situs is an award-winning program package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering. The software supports both rigid-body and flexible docking using a variety of fitting strategies. Situs is developed by Willy Wriggers and coworkers: biomachina.org.

SIR2008:- Direct Method program for the resolution and refinement of crystal structures using single crystal data

SIR2008 Direct Method program for the resolution and refinement of crystal structures using single crystal data), SIR2002 (Direct Method program for the resolution of proteins using single crystal data; can be used also for resolution and refinement of small and medium size crystal structures) and SIR2004 (automatic solution of crystal structures by Direct and Patterson Methods; it can be used both for resolution and refinement of small/medium size crystal structures and for macromolecules with data up to 1.4-1.5 Ang.)

SketchEl:- Molecular drawing

SketchEl is an interactive chemical molecule sketching tool, and molecular spreadsheet data entry application. The feature set provided by the molecular sketcher is largely limited to the minimum features required to conveniently edit diagram representations of small molecule structures. Toolbars, templates, mouse gestures, keyboard shortcuts, utility commands and several view modes are offered in order to make this as convenient as possible. Molecules can be easily interconverted with the ubiquitous MDL MOL file format, though not not necessarily without information loss. Molecule diagrams are rendered interactively in high quality, and can also be exported as SVG graphics.

SMARTCyp:- Predict CYP mediated metabolism

SMARTCyp is a method for prediction of which sites in a molecule that are labile for metabolism by Cytochromes P450 isoform 3A4. It is also a reactivity model which is applicable to all P450 isoforms.The implementation is in the form of a java program using the CDK and JChemPaint java libraries.The program has been tested on Linux, MacOS X and Windows XP, but it should work on any platform.
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.
http://pubs.acs.org/doi/abs/10.1021/ml200246f

Smell-o-mints :- Periodic table

Smell-o-mints is a Periodic table of the elements for the Macintosh. It's not as full-featured as a lot of other Periodic tables out there, but it's free and looks very nice.

smi23D:- Convert SMILES to 3D structures

smi23d consists of two programs that can be used to convert one or more SMILES strings to 3D. The first step uses a program called smisdf which generates a set of rough 3D coordinates using an iterative refinement procedure. These coordinates are then optimized with a MMFF94 force field by mengine to generate a reasonable 3D structure. In addition to generating an optimized structure, the code can optinally calculate some molecular properties such as XlogP, dipole moment and vibrational properties. By default these are not calculated. The resultant coordinates are written in SD format.
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

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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

SnB is a computer program based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data. This program has been used in a routine fashion to solve difficult structures, containing as many as 1000 unique non-H atoms, that could not be solved by traditional reciprocal-space routines based on the tangent formula alone.

Solutions:- iPhone app for calculating concs of buffers

Solutions, Whether you are a chemist, biologist or student, no one likes the calculations
needed before making chemical solutions.

Solver:- Linear programming for Excel

Solver for Microsoft Excel 2008 on Macintosh is available here. You can download it here.

SOMA:- Web-based molecular modelling

SOMA2 is a web-based molecular modelling environment.

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

Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers. For more information about what Sparky does look at the introduction in the manual.

Spartan :- Molecular modelling

The latest Spartan'10 release offers offers all features and methods included in the Spartan Essential Edition, and in collaboration with Q-Chem, provides a full range of post-Hartree-Fock methods including Density Functional, Moller Plesset, Theremochemistry recipes (including the new T1 procedure), and an assortment of Advanced Correlated approaches. Spartan'10 is the dominant version used in academic, government, and commercial research.

SPROUT:- de novo design tool

SPROUT is an effective tool for the design of drug-like, biologically active molecules. It is an interactive system that can assist in several stages of the structure-based rational drug design process.
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

SQLGrinder If you need a tool to access any database that has a JDBC driver (Oracle, Sybase, mySQL, postgresql etc) I highly reccomend this tool, it is a native Cocoa application that has applescript support.

Stardrop:- Platform for supporting drug discovery

StarDrop provides a comprehensive range of features to support design and prioritisation of high quality compounds, including:
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

Sweet J calculates the 3J coupling constant from the dihedral angle and the electronegativity of the substituents using either the Altona equation or a generalized Karplus equation.

Swiss-Pdb Viewer :-Molecule viewer

Swiss-PdbViewer a universal binary is now available.

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

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  • 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
SYBYL-X requires Mac OS X 10.6.x (Snow Leopard) they are already working on Lion support and aim to have it ready when the next Mac OS X update is released. For 3D graphics you might be better having a NVidia graphics card, ATI/AMD work as well, but there are currently some minor driver based issues. So rather than having Hardware 3D on by default for ATI based cards, on detection, hardware stereo will be disabled only for ATI based chipsets. You can however override this using a commandline switch. They also provide KNIME

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nodes for those who would like to include it in workflows. There are a number of licensing options and they are aware that users with multi-core machines would want to be able to take advantage of all cores.

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

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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.