Release Highlights for SYBYL 7.0

A summary of what is new in SYBYL 7.0.

• Architecture, Installation, Licensing
• SYBYL Base
  • Basic Features
  • Force Fields
  • Graphics
• Ligand-Based Design
• Virtual Screening
  • FlexX
  • FlexS
• de novo Design
  • RACHEL
• Biopolymer Modeling
• Chemical Informatics
  • UNITY
• Core Technologies
  • MOLCAD, hint! and ZAP
• Product Retirement
• See also: Release Highlights for SYBYL 6.9.2

Architecture, Installation, Licensing

• SYBYL 7.0 combines software for SGI, Linux, and HP into a single release. A complete reorganization of the software directory structure allows all platforms to share common data, which saves storage space and simplifies the setup and maintenance of site specific variables.
• A new installer and the new architecture of the SYBYL tree allow for the installation of SGI, Linux and HP versions of SYBYL and all associated partner modules into a single directory structure. Partner products and the Tripos Bookshelf are now installed automatically.
• SYBYL 7.0 has been verified under Linux RedHat Enterprise Linux 3.0. It is not compatible with RedHat 7.3.
• New licenses are required for SYBYL 7.0. Licensing in SYBYL 7.0 now uses FLEXlm 9.2 for all licensed products on Linux, SGI, HP and Windows. License borrowing, a new feature, allows a user to check out a set of licenses, disconnect from the network, and use these licenses until the predetermined time period expires. This feature is designed to support laptops which are occasionally disconnected from the network.
• The syntax of a few commands has been altered to provide additional functionality. In addition, many environmental variables were affected by the reorganization. The script sybcompat will help you update your SPL scripts and .sybylrc file to match the new command syntax and the new software architecture.

Cross-Platform Format and Compatibility with Previous Versions

• PIO (Portable Input Output) format overcomes the incompatibility between the two predominant binary formats known as "Little-Endian" (typical on almost all PC compatible hardware) and "Big Endian" (also known as network byte ordering and typical on SGI and HP). More...
• Starting with SYBYL 7.0 most binary files can be shared across platforms. However, this could be accomplished only by changing the format of the following file types: PRODAT, UNITY databases (.tdb), molecular spreadsheet tables (.tbl), QSAR analysis files (.fac, .hier, .jarv, .pls), MOLCAD image files (.sld), Dynamics history files (.his), and contour files (.cnt).

SYBYL Base

Basic Features

• Entry points to the various SYBYL modules have been moved from the Options menu to the new Tools menu.
• More...

Force Fields

• The AMBER 7 force field has been reimplemented as AMBER7 FF99 and AMBER7 FF02 (with polarization energy) to more closely match the force fields provided by the authors of AMBER.
• The Force Field Engine (FFE) is no longer supported. This functionality has been removed from SYBYL.
• More...

Graphics

• The new graphics icon controls the display status, coloring, and labeling of multiple molecules within a single dialog. A satellite dialog manipulates the display of hydrogens. Both dialogs are particularly useful for biopolymers.
• File >>> Print >>> High Resolution Image (SGI only) allows you to create RGB images suitable for publication.
• It is now easier to label atoms: simply hold the CTRL key and right-click on the desired atom(s). The default type of label is atom names. Other choices are atom IDs, types, charges, and substructure names.
• Full screen stereo (FSS), the original stereo mechanism available only on the SGI, is no longer supported. Stereo-in-a-window (SIAW) is available for all supported platforms.
• More...

Ligand-Based Design

Molecular Discovery released new versions of their software:

• Almond 3.3
• VolSurf 4.1

Virtual Screening

FlexX

• FlexX v. 1.13.5 from BioSolveIT is being released with SYBYL 7.0.
• BioSolveIT disabled the DrugScore function because of a patent challenge. This scoring function is no longer accessible from the SYBYL interface.
• FlexX and FlexX-Pharm batch jobs can be submitted to United Devices grid systems.
• More...

FlexS

• FlexS v. 1.11.4 from BioSolveIT is being released with SYBYL 7.0.
• A new mode, called Rigid Superpositioning is now available.
• More...

de novo Design

RACHEL

• A new version of RACHEL (2.06) allows the display of a pseudo-receptor cavity by drawing a mesh-wire cage around the search hits.
• More...

Biopolymer Modeling

A major overhaul of the menu and the addition of several new dialogs provide better support for user task flow.

• Biopolymer Menu Layout.
• Biopolymer Map: from the old to the new.
• The new Prepare Protein Structure dialog performs an analysis of the selected protein and facilitates its preparation for AMBER minimization and for manipulation within SYBYL
• The AMBER 7 force field has been reimplemented as AMBER7 FF99 and AMBER7 FF02 (with polarization energy) to more closely match the force fields provided by the authors of AMBER.
• More...

Chemical Informatics

UNITY

• UNITY is now a SYBYL product.
• UNITY databases are now compatible across SGI, HP and LINUX platforms. Databases created with UNITY 4.4.2 on SGI and HP platforms are readable on all platforms in SYBYL 7.0.
• The database LeadQuest.tdb has been renamed LQSample.tdb
• The old (non Java-based) Hitlist Manager is no longer available.
• More...

Core Technologies

MOLCAD, hint! and ZAP

• It is now possible to map hint! lipophilicity and ZAP electrostatics properties onto MOLCAD surfaces.
• More...

Product Retirement

Tripos has discontinued the distribution of the following functionality, effective with the SYBYL 7.0 release. Associated dialogs and commands are no longer available within SYBYL.

• HDisq
• Topkat
• Force field engine
• MM2 and MMP2
• ZINDO

SYBYL 7.0 is the last release of:

• SYBYL on HP-UX