Biologics Suite 2012 Update 2 Release (BioLuminate 1.0.518 - Dec 2012)

• Platform Support

  See the Installation Guide for additional requirements for specific operating systems.

  Linux

  Linux-x86 (32-bit) executables: RedHat Enterprise Linux (RHEL) 3.9, 4.x, 5.x and 6.x CentOS 3.9, 4.x, 5.x and 6.x SUSE SLES and SLED 9.x, 10.x (except 10.3), and 11.x Ubuntu 10.04 LTS The 32-bit executables are supported on 64-bit operating systems with the appropriate compatibility libraries. Click here for important information on Linux 32-bit support. NOTICE: We have decided to extend support for Linux 32-bit to include Suite 2012. However, Suite 2012 will be the last release for which Linux 32-bit versions of our software will be supported. Major releases after Suite 2012 will NOT include 32-bit Linux support. Only 64-bit Linux operating systems based on glibc version 2.5 or later (such as Red Hat Enterprise Linux/CentOS version 5.2 or later) will be supported after Suite 2012. This also means Suite 2012 will be the last release with support for RHEL/CentOS 3.9/4.x/5.0/5.1 and SUSE SLES and SLED 9.x, 10.x (except 10.3, which is not supported). We recommend using the 64-bit version of Suite 2012 unless you specifically need support for one of these older operating systems. If you do need support for one of these older operating systems, you must use the 32-bit version of Suite 2012. Linux-x86_64 (64-bit) executables: RedHat Enterprise Linux (RHEL) 5.2 and later 5.x 64-bit versions, 6.x CentOS 5.2 and later 5.x 64-bit versions, 6.x SUSE SLES 11 and SLED 11 64-bit Ubuntu 10.04 LTS

  Windows

  Windows 32-bit executables: Windows 7, 32-bit and 64-bit Windows Vista SP1, 32-bit and 64-bit Windows Server 2008 and 2008 R2, 64-bit Windows XP (Home or Pro version) SP2 or SP3, 32-bit only Windows 64-bit executables: Windows 7, 64-bit Windows Vista SP1, 64-bit Windows Server 2008 and 2008 R2, 64-bit

  Mac

  Intel processor Mac OS X version 10.6 (Snow Leopard) or 10.7 (Lion); 64-bit only

• New Features

  The Schrödinger Biologics Suite, featuring BioLuminate

  A new, easy-to-use, software package targeted towards biologics and proteins

  Changes for the Update 2 release:

  • Protein docking runs natively on Mac OS X and Windows
  • Residue scanning calculations from the command line fully supported
  • New color code that matches aggregation prediction output in Multiple Sequence Viewer (MSV)
  • Improvements to Residue Scanning panel
  • User manual available
  • Various bug fixes and performance improvements

  
  Changes for the Update 1 release:

  • New Protein-Protein Docking
  • New Protein Aggregation Surface for predicted potential sites of aggregation
  • Enabled Residue Scanning jobs to run on multiple processors
  • Enabled Residue Analysis jobs to run in the background
  • The Humanize Antibody module now uses a database of human-only antibodies for homologs
  • Fixed bug in Residue and Loop Mutation that resulted in some loop residues not having side chains
  • Fixed the definition of the glycosylation motif
  • New Quick Start Guide

  
  Features included in general release:

  • General Protein Modeling
    • Simple homology modeling panel for rapid model building
    • Advanced homology modeling offering additional controls
    • Both fast and advanced loop prediction methods
    • A complete set of protein sequence analysis tools
      • BLAST/Pfam searches, multi-sequence alignments, advanced annotations, antibody annotations
    • Protein property and secondary structure prediction from sequence using the SCRATCH suite
    • Mutation modeling
      • Simple interface for residue and loop replacement
    • Consensus visualization of protein families and homologs
    • Calculation and display of low-mode large-scale protein motions
    • Interactive protein structure quality analysis
  • Protein Design
    • Residue mutation scanning
      • Affinity
      • Stability
      • Reactivity
      • Additional properties
    • Calculation of residue-based properties
      • Potential energy, solvent accessible surface area, hydrophobicity, and hydrophilicity
    • Cysteine scanning
      • Automated identification of residue mutations that can make or break disulfides
    • Mutation suggestions based on analysis of homologs
    • Identification of reactive hot spots (proteolysis, glycosylation, deamidation, and oxidation)
  • Antibody Modeling
    • Antibody-specific homology modeling workflow
    • Antibody database management tools
    • Automated rapid prediction of CDR loops from sequence
    • Validated ab initio method for antibody CDR loop prediction
  • Advanced Simulation Tools
    • Alpha-helix stability/melting analysis from molecular dynamics
    • Free energy perturbation for mutation predictions
    • QM/MM calculations for binding site reactivity
  • Interface
    • Workspace integrates familiar PyMOL design elements to reduce learning curve
    • Menus conceived with a biologics focus
    • A workflow/task-based design paradigm