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The web portal [41] freely allows to build CoMFA and COMBINE models readily handling the classical steps that need to be accomplished up to the final optimization and validation of robust models. The flowchart consists of a careful selection and alignment of training and test set molecules, calculation of molecular interaction fields (MIFs), statistical analysis, interpretation of results and graphical plots. Once these steps have been assessed, the model can be applied to predict the activity of untested molecules or to design new chemical entities with either LB or SB approaches.

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Pearson correlation analysis was performed using SPSS software to study the relationship between the binding free energies and the molecular weights, KOA, BCF, t1/2, and IC50 values of the PCBs. The KOA [45], BCF [46], t1/2 [47], and IC50 [48] values were obtained directly from the literature. The binding free energies were significantly correlated to the molecular weight, KOA, BCF, t1/2, and IC50 values when the P value was less than 0.01. The binding free energy was significantly correlated to the molecular weight, KOA, BCF, t1/2, and IC50 when P was more than 0.01 but less than 0.05. The binding free energy was not significantly correlated to the molecular weight, KOA, BCF, t1/2, or IC50 when P was more than 0.05.

The free version is an old version that is no longer supported. Academic and Pro are the latest supported versions with many new features added, including 64-bit support for Windows and Linux. Complete list of new features and bug fixes is available in PyRx 0.9.x Release Announcements on our Blog. There is no feature difference between Academic and Pro. Academic is discounted for academics and nonprofits who can use coupon code ACADEMIC to get 50% off. The license is perpetual and there are no subscription fees. This software can be installed on multiple devices in the same lab. Please do not distribute PyRx to more than 10 people in the same lab for commercial purposes. There is no limit on the number of computers Academic users can install PyRx in the same lab. Please do not share PyRx outside of your lab. If you need to distribute PyRx to more than 10 people for commercial purposes, you need to choose the Enterprise option that includes PyRx for Windows, Linux and Mac OS X.

Produced by Stewart Computational Chemistry and free to academic users, MOPAC2012 has been integrated to work with Schrödinger software but only MOPAC2016 is available for downloading. Instructions for modifying 2016 to 2012: Copy MOPAC2016.exe and rename the copy MOPAC2012.exe. Copy "password for MOPAC2016" and rename the copy "password for MOPAC2012" You should then have two MOPAC executables and two passwords. Then try running the Schrodinger software.

Listed Alphabetically AbM - ALCHEMY - CAChe - Cerius2 - Chem3D - GAMESS - Gaussian - HyperChem - Insight II - MOPAC - Nemesis - PCModel - SPARTAN - TurboNMR - Unichem - ZINDO AbM - an integrated suite of programs for antibody structure modeling. Itcombines the benefits of knowledge databases with ab initio methods, permittingyou to model the tertiary structure of an antibody starting with its primarysequence. -- Oxford Molecular Group ACD/Labs is a collection of Windows-based structure drawing and analysistools. Programs available include ACD/ChemSketch, ACD/Tautomers (check andgenerate predominant tautomeric forms), ACD/LogP, ACD/CNMR and ACD/Dictionary.-- Advanced Chemistry Development Inc. ACES II is an ab initio Molecular Orbital program which uses many-bodyperturbation theory to derive correlation energy. -- Rodney Bartlett, QuantumTheory ProjectGIAO ACM (Adiabetic Correction Method) replaces part of DFT exchange with exactexchange from HF. ADAPT (Automated Data Analysis using Pattern Recognition Toolkit) ADF (Amsterdam Density Functional) -- Bert te Velde, Vrije Universiyteit AIPHOS (Artificial Intelligence for Planning and Handling Organic Synthesis)Computer Assisted Synthesis -- K. Funatsu ALCHEMY-II is a set of IBM based programs for direct CI and MCSCF on smalland medium sized molecules. One-particle density matrices, One-electronproperties, natural orbitals, transition density matrices. -- Michael Dupuis,IBM Corporation Alchemy 2000 (3, low end Sybyl relative) is a desktop molecular modelingsystem for PC (DOS and Windows) and Macintosh computers. Provides structurebuilding, comparison, optimization, and display. Systematic & MCsearches., protein builder -- Tripos, Inc., :MM2, MM3, SybylMP3Cons:charge calculations unreproduciblesubstitutes for missing parametersFile Formats:Sybyl.molBrookhaven.pdbChemDrawHyperChemMDLSMILESSciVisionAlchemy III.molDimensions: 3500+ atomsProperties:IR spectraThermodynamicsdipole momentVdW energysteric energydistanceangleSciPolymer-polymer property QSPRSciQSAR-QSPR spreadsheet toolSciProtein-protein structure seq's & DBSciLogP-logP QSPR AMBER (Assisted Model Building using Energy Refinement). A suite of programsfor molecular mechanics and molecular dynamics simulations. Designed primarilyfor proteins and nucleic acids. AMPAC (Austin Method PACkage) Computer code that first presented the AM1method to the world. A semiempirical quantum mechanics program developed byMichael Dewar and co-workers. The program contains the MINDO/3, MNDO and AM1Hamiltonians. RHF (Restricted Hartree-Fock) and UHF (Unrestricted Hartree-Fock)methods. Extensive CI (Configuration Interactions). Options permit geometryoptimization, calculation of transition state geometries and activation energybarriers, calculation of force constants, normal mode analysis, etc. -- QCPE506 AMPAC 6 (8) with graphical user interface Z-Matrix editorsimulated annealingsymmetry group assignment CHAINPATHEFESPAMSOLCODESSA - QSPR toolFile Formats:Mopac InputGaussianHyperchemParameters:MINDO/3, MNDO, PM3, AM1SAM1MNDOCProperties:IR (Force) SpectraESRNLOHOMOLUMODistanceAnglechargesmolar volumemolar surface areaovalitydipole momentUV (CI) AMSOL AMPAC with explicit solvation effects -- Chris Cramer and Don Truhlar,The University of Minnesota & QCPESM2 Basis:AM1aqueousAtoms:HC - FP - ClBrSM5 Basis:230 solutes90 solventsAcc'y:[Delta]G(transfer)+/-0.7 kcal/mol Anaconda - an interactive molecular similarity for visualcomparison/alignment of surface properties and pharmacophore discovery. --Oxford Molecular Group Apex-3D is a rule-based QSAR program. -- BIOSYM/MSI Art of Science is a collection of EPS images prepared especially for thescientific community for import into page layout and word processing andprograms including Microsoft Word. -- SoftShell ARITVE is a program for modeling amorphous mean tridimensional structure by aRietveld-type approach (refining atomic coordinates against neutron or/andX-ray interference functions). It is a freeware. FORTRAN sources are availablefor DEC-ALPHA-AXP running VMS. -- ASP is a fast, automatic similarity assessment program which calculatesmolecular similarity based on spherical projection of electrostatic, steric,lipophilic or refractive properties. -- Oxford Molecular The Babel file conversion program. BioGraf was formerly available from MSI but has been discontinued as aproduct line. Bionet - an on-line timesharing system for DNA and protein sequence analysis.-- Oxford Molecular Group BIOPROP is a generalized, programmable neural network simulator forpredicting protein structures. Designed for use on mainframe andsupercomputers, however, the Fortran 77 code can be modified for use onpersonal computers. -- Office of Technology Licensing, Berkeley BOSS (Biochemical and Organic Simulation System). Monte Carlo statisticalmechanics simulations of organic molecules, complexes and reactions insolution. CACAO (Computer Aided Composition of Atomic Orbitals) is a package ofelectronic structure programs for the calculation and analysis of molecularorbitals. The package consists of an EHC program (SIMCON), an orbital analysisprogram (MOAN) and a display program for atomic orbitals (CACAO). The programsrequire at least a 286 PC with math co-processor. -- Davide M. Proserpio,Universita di Milano CAChe WorkSystem (10, user friendly general purpose modeling) suite ofmodules covering range of computational chemistry methods. -- Oxford Molecular, - Editor & CAChe Translators3-D sketchPolymerizerCrystal Builder12+ search variablesSequential searchForce Field toolsFile Formats:MDL .molTripos .molBrookhaven .pdbCCSDBChem3D (original)TribbleShelxMopac InputZINDO Input - Dynamics: performs molecular dynamics with the augmented MM2 forcefield. - ExtHuckel: Extended Hückel calculationsAtoms: Gauge Including AOs) usual AO'sare multiplied by a "gauge vector" to provide "gauge-invariant" magneticproperties.Acc'y:([sigma] in PPM w 6-311G** perturbed HF)P+/-32C+6H+6.1% GMMX is available as part of PCModel, a structure building, manipulation andminimization program. -- Serena Software GRADSCF is an ab initio quantum chemistry program which has been designed forthe Cray environment. Its major function is to provide energies and propertiesfor a variety of molecules of chemical interest. Gradscf runs under the Unicosoperating system. -- Dr. Andrew Komornicki, Polyatomics Research Institute GRID is a computational procedure for detecting energetically favorablebinding sites on molecules of known structure. It may be used to study arraysof molecules in membranes and crystals or macromolecules such as proteins. Theenergies are calculated as the electrostatic, hydrogen-bond and Lennard Jonesinteractions of a specific probe group with the target structure. GRID candistinguish between selective binding sites for different probes. Input forGRIN is prepared and checked by GRID. Display of results is through outputfiles produced by GRID. The programs are written in Fortran 77 and run on allcomputer systems. -- Peter Goodford, Molecular Discovery Ltd. GROMOS (GROningen MOlecular Simulation package) is a molecular mechanics anddynamics program developed by W. F. van Gunsteren and co-workers at TheUniversity of Groningen. -- Biomos B. V., University of Groningen Molecular & Stochastic DynamicsPerturbation ThermodynamicsGROMOS FF Basis:proteinsnucleotidessugars GroupServer - a suite of computational tools for molecular modeling,networked to the CAChe WorkSystem. -- Oxford Molecular Group GULP (General Utility Lattice Program) general lattice simulation withperiodic boundary conditions and Ewald sums for electrostatics. Calculatesproperties, or inverse operation to fit potentials to structure, properties, QMpotential surfaces. Minimize energy with P, V and optical constraints. Locatephase transition states. (Phase diagrams, charge defect correction.) -- JulianGale, Imperial CollegeProperties:Crystal lattice energyEntropyFree EnergyHeat capacityElastic constantsDielectric constantsPhonon frequenciesIR activitiesElectric field gradients GVB (Generalized Valence Bond) - Bill Goddards "laid back southernCalifornia wavefunctions." Equivalent to MCSCF correlation treatment: 2configurations used to represent each e- pair and solved for 2 associatedorthogonal functions. Hingefind is a new algorithm to determine and visualize protein domainmovements by comparing two structures. HINT (Hydrophobic INTeractions) a program for calculating and visualizinghydrophobic and hydrophobic interactions of biomolecular specie. -- eduSoft. HMO-Plus1.5Atoms:B - FSi - Cl Properties:Secular DeterminantEigenvaluesTotal energydelocalization energyPolarographic half-wave reduction potentialEigenvectorsCharge densities[pi]-dipole momentBond lengthsElectron density - bond order matrixAtom-atom polarizabilitiesSuperdelocalizabilities - Electrophilic - Radical - NucleophilicFree valences HONDO7 is a semiempirical molecular orbital program with single configurationSCF (closed shell RHF, spin restricted UHF, restricted open shell ROHF),generalized valance bond (GVB) and general multiconfiguration SCF MCSCFwavefunctions as well as configuration interaction (CI) wavefunctions. Writtenby Dupuis, Watts, Villar and Hurst. -- QCPE 544 HyperChem 4.5 (3, general modeling system with potential) is a building,optimization, manipulation and display program for PC and SGI. -- HyperCubeInc. Originally code for parallel computing serialized to PC product.solvent boxMDab initio SCFMP2File Formats:MDL .molTripos .molBrookhaven .pdbMopac InputCCSDBDimensions:20,000+ atomsParameters:MM2AmberBIO+OPPLS Basis:liquidssolutionsab initio calc'ns on 100 organicsEHTMNDO (w/o Cr, Zn, Br, Sn, Hg, Pb?)MINDO/3AM1 (w/o Hg?)PM3 (w/o Hg, Tl, Pb, Bi?)CNDOINDO/1 (w/o As, Br, I?)INDO/SProperties:Dipole momentIPIR (Force)UV (CI) - Chem PlusCrystal builderrenderingsMC searchbiomoleculeslogPscripts - HyperChem Lite - HyperNMRSCF-MOmagnetic shielding (shifts)nuclear coupling ICON8 and FORTICON8 provide Extended Hückel calculations for moleculescontaining 50 (or fewer) atoms which contain S, S and P and S,P and Delectrons. Written by Howell, Rossi, Wallace, Haraki and Hoffmann. -- QCPE 344 Iditis - This package provides instant access to protein motifs,substructures and interactions buried in the Brookhaven databank, 500descriptors. -- Oxford Molecular Group corrected PDB database500 descriptors Iditis Architect - suite of programs that lets you create protein structuredata for inclusion in the Iditis database. -- Oxford Molecular Group IG Suite - these tools allow you to do DNA and protein sequence analysisusing Sun and VAX workstations. -- Oxford Molecular Group IMSL Libraries IMSL supplies two libraries of subroutines for graphics,Mathematics and Statistics. IMSL/IDL is an array oriented interactive commandlanguage complete with graphics and a robust set of mathematical, statistical,image processing and signal processing functions which allow visual explorationof numerical data. Exponent Graphics is a library of graphical subroutines thatalleviates the task of coding low-level graphics primitives. The IMSL Librariesis an extensive set of 900 Fortran subroutines for applications in generalapplied mathematics, special functions and for analyzing and presentingstatistical data. Libraries are also available for C programming needs. All ofthe IMSL software runs on a wide variety of platforms. -- IMSL, Inc. Insight II (6, specialized modeling on workstations) is a 3D graphicalenvironment for the creation, modification, manipulation, display and analysisof molecular systems and related data. User interface integrates array ofbuilder modules, development tools, force fields, simulation and visualizationtools with tools specifically developed for applications in the life andmaterials sciences. -- BIOSYM/MSI, spreadsheet"Open Interface" - Affinity: automated docking of ligands to receptors in thestructure-based drug design process. Calculations include an implicit solvationterm, and the component effects of this term, and of other energeticpartitions, can be viewed graphically. - Amorphous Cell: constructs and analyzes models of bulk amorphoussystems such as polymers and glasses. Investigate properties such as cohesiveenergy, chain dimensions, chain packing, and local dynamical behavior.atomisticglassy or meltIRcohesive energy densityself diffusionelasticitycorrelation functionsolubility parameter - Apex-3D: identifies pharmacophores and active conformations from aset of biologically active and inactive compounds to predict the activity ofnew compounds. - Biopolymer: constructs models of peptides, proteins, carbohydrates,and nucleic acids for visualizing complex macromolecular structures and for usein further simulation work. - CFF95: advanced Class II force field used to optimize DNA, RNA,carbohydrates, lipids, proteins, peptides, and small-molecule models, giving ahigh confidence level for calculations in drug discovery, protein design,genomic theraputics, NMR spectroscopy, and X-ray crystallography. - Characterize: simulates, displays, and interprets a wide variety ofanalytical data: HRTEM, NMR, diffraction, IR Raman, EXAFS, and Morphologydata.XRD, ND, ED29Si NMREXAFSCrystal morphologyIR, RamanPore characterization- Consensus: builds a 3D model of a protein from its amino acidsequence and the known structures of related proteins using distanceconstraints derived from the reference protein structures. - Converter: builds 3D models from 2D structural database output. - Crystal Cell: study and characterize crystal structure, stability,and mechanical properties. minimize packing energy w/ MMvibrational dispersion curveentropyheat capacitymechanical properties - DBAccess: uses a hypothesis that may include binding features,structural and property constraints, as a search query against databasescontaining hundreds of thousands of molecules to select molecules for trial orto the guide synthesis of new compounds. Includes the Maybridge catalog andthe NCI database. - DeCipher: powerful and flexible program for high-level analysis ofmolecular structure and the results of molecular dynamics simulations. - DelPhi: calculates electrostatic potentials and solvation energiesof both large and small molecules, including nucleic acids. Examine theeffects of charge distribution, ionic strength, and dielectric constant on theelectrostatic potentials of macromolecules. - Discover: simulation program available within Insight II. Itincorporates a range of well validated forcefields for dynamics simulations,minimization, and conformational searches to predict the structure, energeticsand properties of organic, inorganic, organometallic, and biological systems.Implements IPC (Inter Process Communications), which allows users to instructDiscover to turn processing control over to external programs, and retrieve theresults of those external processes, incorporating them into the continuingDiscover computations. - DMol: quantum mechanics module for fast, reliable, quantitativepredictions of molecular structure, energetics and properties for ground andtransition states. Employs advanced density functional theory. COSMO is acontinuum dielectric solvation model implemented in DMol to accurately computethe structure and properties of molecules in a solvent environment usingquantum mechanics.- DSolid: provides accurate simulation of molecules, molecular crystals,and surfaces. An adaptation of the DMol program to compute structural andvibrational properties as well as electron densities and molecular orbitals forperiodic solids. - ESOCS: (Electronic Structure Of Closed-packed Solids) calculatesthe electronic and magnetic properties of solids, including electronicstructure of defects, optical absorption and reflection spectra, and magneticproperties of materials. Applicable to metals and alloys, the pigmentindustry, and for optimizating and designing magnetic materials.all purposeperiodic electronic structure -

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