Portland, OR, June 18, 2007 -Schrödinger is pleased to announce the debut release of PrimeX, anintegrated package for accurate protein crystal structure refinement.PrimeX joins Schrödinger Suite 2007, which was released earlier. Pleaseread below for more information about PrimeX and the rest of the 2007Suite. Look for further announcement of KNIME Extensions in the comingweeks. Click here for a PDF of the Product Feature list for Schrödinger Suite 2007. To download the new release, please visit the Support Center .New ProductsPrimeX 1.0 [Visit Product page] PrimeX performs refinement of protein crystal structures from initial model to finished coordinates. Rigid-body refinement, individual coordinate and B-factor refinement, and grouped occupancy refinement can be performed in reciprocal space, with maximum likelihood and least-squares targets. Real space refinement tasks build and optimize loops, fit side chains, and facilitate the placement of water and small molecules. Protein structure validation tools evaluate molecular geometry and model fit to electron density. Some of the features that distinguish PrimeX are:building of loops based on Prime protein structure modeling and guided by electron density fit flexible placing of ligands and other small molecules into electron density using Glide docking technology truncated Newton minimizer restraints based on the advanced OPLS force field execution of all operations through a logical user interface integrated into Maestro access to operations through command-line input as well as scripting with Pythonstep-by-step organization of refinement statistics in the Maestro Project Table MCPRO+ 2.0MCPRO is a well-validated simulation package from Prof. Bill Jorgensen (Yale) that performs Monte Carlo statistical mechanics simulations of ligands, peptides, proteins, and nucleic acids in the gas phase or in solution. Accurate free energy changes are computed from statistical perturbation theory to generate relative or absolute free energies of binding for protein/ligand complexes, reaction profiles, potentials of mean force, and free energy profiles for rotation about a dihedral angle. A powerful user interface and use of the Schrödinger job control facility makes setup and monitoring of MCPRO simulations simple. Key features include:Wizard-based interface for users to calculate relative binding free energies for protein/ligand complexes via accurate free energy perturbation (FEP) theory Prediction of protein/ligand binding free energies using linear response methodology Energy minimization in Cartesian or internal coordinates Full range of solvation options including periodic explicit solvent boxes or solvent caps and the GB/SA implicit solvent model Partition coefficient calculation in a range of organic solvents Automatic atom-typing with OPLS_2001 or OPLS_2005 of macromolecular species Utilize quantum mechanical charges or those from the OPLS force fields for ligand species Boltzmann-weighted trajectories from NPT or NVT Monte Carlo sampling, which can be used analogously to Molecular Dynamics trajectories Near real-time monitoring of key properties during distributed FEP simulations Graphical analysis tool to examine plots of key properties throughout FEP simulations as functions of the number of configurations and perturbation windows Integration with the Schrödinger Job Control facility, which provides job distribution across multiple CPUs and built-in job monitoring and job restarting KNIME Extensions 1.0 (Coming soon) KNIME (www.knime.org ) is an open source pipelining program that provides a graphical interface for building workflows. Most of Schrödinger's tools have been integrated as KNIME Extensions, providing components within KNIME for building workflows.XP Visualizer The XP Visualizer displays a representation of the individual terms that comprise the XP GlideScore in the Maestro Workspace, using intuitive graphical elements and highlighting of the contributing receptor and ligand atoms. This new lead optimization tool provides clues as to which portions of a ligand are most important for binding, thus assisting modelers in designing more potent inhibitors. The XP GlideScore terms, which cover a wide range of interactions, are:ChemScore lipophilic pair term and fraction of the total protein-ligand vdW energy Hydrophobic enclosure reward Reward for hydrophobically packed H-bond Reward for hydrophobically packed correlated H-bonds ChemScore H-bond pair term Electrostatic rewards SiteMap ligand/receptor non-H-bonding polar/hydrophobic and hydrophobic/hydrophilic complementarity terms Π-Π Stacking reward Reward for Π-cation interactions Reward for Cl/Br in hydrophobic environment that pack against Asp/Glu Reward for ligands with low molecular weight Polar atom burial and desolvation penalties, and penalty for intra-ligand contacts Penalty for ligands with large hydrophobic contacts and low H bond scores Penalty for exposed hydrophobic ligand groups Rotatable bond penalty More information on these terms can be found in Friesner, et al. J. Med. Chem., 2006, 49, 6177.Updates to Existing ProductsCombiGlide 1.5 [Visit Product page] Core/scaffold hopping - identification of cores compatible with side chains of a lead compound Improved robustness of overall workflow Considerable speed-up of overall process Better enforcement of user-specified core position More accurate core positioning without user specification User-accessible validation procedure: computation and read-out of enrichment factors based on user-supplied list of known active compounds Tools to prepare a filtered or focused reagent collection from a highly diverse collection Chemical-feature analysis: quantitative assessment of extent to which specific chemical features focus at the various combinatorial sites Epik 1.5 [Visit Product page] Available on Windows Charge spreading: interpolation between different alternate formal charge versions for heteroaromatic atoms and substituents More functional groups parameterized for acid and bases, substituents, and heteroaromatic atoms Sequential pKa prediction Upper and lower limits on recorded pKa values Additional tautomerization types supported Glide 4.5 [Visit Product page] Available on Windows New SP 4.5 GlideScore, with selected motifs from XP GlideScore for improved performance in virtual screening Updated XP 4.5 GlideScore, which includes additional hydrogen bond motifs Automated post-docking minimization and rescoring by GlideScore, to generate docked ligand poses with low internal strain energy Restriction of the position of a core chemotype in docking via industry standard SMARTS patterns Refinement of protein-ligand complex geometries using SP or XP GlideScore Expanded ability to calculate RMSDs of docked poses against a reference ligand or a partial topology of the reference ligand, specified via industry-standard SMARTS patterns Improved performance for docking with multiple constraints Simplified output from docking and handling of Glide grids as a single file Jaguar 7.0 [Visit Product page] Available on Windows Parallelized vibrational frequency calculations New density functionals: PWB6K, PW6B95, M05, and M05-2X SM6/CM4 solvation model Linux-ia64 version is supported for all Itanium2 machines running a compatible Linux operating system Time-dependent density functional theory (TDDFT) 2D torsional scan data can be plotted in Maestro New pKa functional group parameters Improved python script for calculating binding energies of hydrogen-bonded systems Reduction in I/O, resulting in speed up of very large jobs Display of QM molecular dipole in Maestro Automatic restart of SCF with higher accuracy settings if the default criteria do not lead to convergence Optional Mulliken analysis after each step in an optimization Conversion of Jaguar output files into Maestro files containing calculated properties New solvents for solvation calculations Molecular orbital plots for geometry scans LMP2 jobs on systems with up to 400 occupied orbitalsIncreased memory limit for NBO to support larger molecules Comparison of ESP maps for different molecules in Maestro using ESP normalized to the number of electrons Projection of a wave function obtained with a mixed basis set onto a different mixed basis set LigPrep 2.1 [Visit Product page] Available on Windows Ring conformations: (1) addition of many more ring templates; (2) user extension of ring template library Additional tautomer patterns Panel to set up LigParse filter files Enforces chirality correlations in fused ring systems MacroModel 9.5 [Visit Product page] Available on Windows General speed enhancements for most calculations, particularly on AIX Solvation model update for OPLS_2005 Enhanced conformational sampling for rings: (1) using saved templates, (2) FLAP, ring vertex reflections through the ring ASL/SMARTS definition for substructures Maestro 8.0 [Visit Product page] Improved support for backend applications on Windows Significant enhancement to Project Table performance Customizable menus Improved job monitoring Ramachandran plots Support for alternate PDB positions and crystal mates View animation (smooth spot centering, fit to screen, etc.) Ability to color molecular surfaces by the electrostatic potential Support for Boolean operations on surfaces (union, intersection, and difference) Independent clipping of surfaces and structures Clipping by atom selection (for example, clip the receptor, but not the ligand) Improvements to all surfaces types (solid, mesh, and dot) Wrapping and image saving in the sequence viewer Easier adjustment of torsions Mouse scroll wheel support for a wide range of operations Use of arrow keys to quickly view in the Workspace successive/previous Project Table entries Ability to draw arbitrary objects in the workspace via Python scripting Support for ZIP-compressed Projects (.prjzip) Phase 2.5 [Visit Product page] Databases:Significantly improved searching speeds Low-memory hit list management, which allows much larger "maxHits" values Checkpoint mechanism to store partial search results and allow easy restart of jobs that die due to hardware failure Searching of databases that are not mounted on local machine One-to-many feature matching (OR logic) Negative feature matching (NOT logic) On-the-fly expansion of matching conformations to improve fit Database creation from SMILES Export/search database propertiesIn-Place Scoring:External file and Project Table searching Pharmacophore perception Hypotheses:Visualization and alignment of multiple hypotheses Project Table access to hypotheses Exporting of multiple hypotheses Click-and-drag adjustment of excluded volume positions Graphical interface for receptor-based excluded volumes Feature Definitions:Mapping of aromatic rings as both H and R Transfer of H, R default patterns to custom features Control of projected feature distances on a per-pattern basis Prime 1.6 [Visit Product page] Implicit membrane model with a graphical interface for setting up the membrane region Improved robustness General speed-up Updated protein analysis tool QikProp 3.0 [Visit Product page] Available on Windows Additional descriptors, including Jorgensen's drug-like Rule-of-Three Use of molecular property databases to improve prediction of octanol/water partition coefficient (logP) and aqueous solubility (logS) Improved % Human oral absorption qualitative prediction using a decision tree Automatic identification of compounds in a database most similar to processed ligands through similarity in property space QSite 4.5 [Visit Product page] Link atom method (also called "hydrogen cap method"). This method allows QM/MM jobs to be run on virtually any kind of molecular system, including proteins, DNA/RNA, as well as non-biological systems Simplified input file format, which allows quick modification of input via scripting or where a GUI is not available Display of any defined QM region when input or restart files are read into Maestro Writing of QM ESP charges to Maestro file for use with other programs, such as Liaison or Glide Projection of a wave function obtained with a mixed basis set onto a different mixed basis set Strike 1.6 [Visit Product page] Additional uni- and bivariant descriptors calculated Factor analysis interface to examine hidden relationships in data Updates to Existing Solutions/WorkflowsInduced Fit Docking [Visit Solution page] Automated side-chain trimming based on predicted flexibility Job Control and Licensing Automatic retry of failed subjobs (such as in para_glide) License checking/requeuing for selected queuing systems Ability to start local jobs from Maestro with lower priority Many improvements to Grid-computing environment QM-Polarized Ligand Docking [Visit Solution page] Use of H-bond constraints Ability to start with pre-docked poses More robust running of large jobs Reduced size of job directories QM charges in solution or gas phase Protein PreparationFully integrated into Maestro Water sampling Improved speed of Protein Assignment Restrained minimization with heavy atoms fixed Import of PDB files from the web Automatic preparation of structures for use in Prime Support for remote job submission Virtual Screening Workflow (VSW)Ensemble docking capabilities Enhanced filtering options More scoring options (SP/XP Score-in-Place and Minimize-and-Score) Optional MacroModel conformational sampling of large rings New Python ScriptsFlexible superposition of molecules via pharamaphore alignment Interactive manipulation and interaction energy calculation of ligand/protein complexes via MacroModel Fragment-based scripts for fragmentation, joining, and scoring Entropy calculation analysis of ligands based on work of Ruvinsky Pose filtering based on receptor interactions Simplified interfaces for Glide docking calculations For a complete list of Python scripts, visit https://www.schrodinger.com/page21/