March 2008
| YASARA supports side-by-side stereo for flat-screens that do not work with shutter glasses.
|
January 2008
| A scene content browser with context menus in the top right head-up display allows to easily and quickly navigate and modify the scene. |
November 2007
| YASARA has a new Python interface: stand-alone Python scripts can simply import the new YASARA Python module and directly use all YASARA functions. |
October 2007
| YASARA supports multiple structural alignments using Arun Konagurthu's MUSTANG program,
which has been fully incorporated.
|
September
2007
| YASARA performs local Smith&Waterman and global Needleman&Wunsch sequence alignments and can use them to superpose structures.
|
July 2007
| Douglas Theobald contributes the THESEUS maximum likelihood algorithm to superpose bundles of NMR structures fully automatically,
putting more emphasis on the structurally conserved regions.
|
May 2007
| YASARA features a new multi-threaded high-speed algorithm to draw molecular surfaces. Just like Van der Waals and solvent accessible surfaces,
they now adapt in real-time to moving atoms.
|
March
2007
| YASARA is now available for Mac OS X
, including special support for Mighty Mouse and MacBook track pad.
|
February 2007
| YASARA's OpenGL graphics engine supports
real-time shadows and ambient lighting, even on old notebooks that do not have pixel/vertex shaders
(OpenGL 1.2).
|
January 2007
| YASARA gets a newly styled look that also adapts to your current operating system
.
|
December 2006
| YASARA now supports parallel molecular dynamics simulations on multiple CPUs
.
|
September 2006
| The new YAMBER3 force field is available, providing more accurate molecular dynamics simulations.
|
June 2006
| YASARA can calculate force field energies individually per unit
(atom, residue, molecule, object) to locate regions of interest.
|
March 2006
| YASARA uses eigenvector analysis to calculate angles and dihedrals between groups of atoms like helices or planar side-chains.
|
January 2006
| The AutoSMILES algorithm provides fully automatic force field parameter assignment for organic molecules,
e.g. unusual amino acids or ligands. 98% of the PDB can now be simulated at the touch of a button.
|
November 2005
| A new algorithm combining graph theory with chemical knowledge on valence ambiguities and preferred tautomers
improves typing of hetero-polycycles, and makes it straightforward to handle complex ligands in PDB files.
|
October 2005
| Structure based alignments are now available in Windows and Linux using the methods CE,
Multiprot and Sheba thanks to a web-server plugin developed by Emmanuel Bettler and Mikael Roche at IBCP Lyon/France.
|
September 2005
| Molecular graphics can be augmented with all kinds of solid objects: spheres,
ellipsoids, cubes, boxes, cylinders, cones, prisms and pyramids. |
August 2005
| YASARA now includes a SMILES based library of chemical knowledge about pH dependent bond orders and protonation patterns,
making it possible to type bonds and add missing hydrogens to any organic molecule at any pH from
0 to 14.
|
July 2005
|
YASARA imports OpenOffice Impress and Microsoft PowerPoint presentations and makes it easy to add molecular animations.
|
May 2005
| YASARA calculates Van der Waals, molecular and solvent accessible volumes
|
April 2005
| The YASARA/WHATIF Twinset adds structural alignments, a hydrogen bonding network optimizer,
a regularizer for covalent geometry and the option to analyze backbone dependent rotamer distributions.
|
February 2005
| The YASARA/WHATIF Twinset is released. YASARA can now perform
20+ different WHAT_CHECKs: bonds, angles, torsions, omega angle, Ramachandran plot,
side-chain rotamers, proline rings, chirality, planarity, backbone conformation,
peptide-plane flips, bumps, 3D packing quality, inside-outside distribution, unsatisfied H-bonds,
or flipped Asn/Gln/His side-chains.
|
January
2005
| YASARA encodes MPEG movies from normal or ray-traced screenshots. Can be pasted into Powerpoint etc.
|
December 2004
| A fast implicit solvent model using a first order boundary element approach allows to calculate solvation energies.
|
November 2004
| A flexible implementation of multi-dimensional tables including visualization makes all kinds of data analysis very easy.
|
October 2004
| Heavily improved surface analysis becomes available. The
'FirstSurf' command allows to subdivide surfaces, the new operators 'with distance from surface' and
'with contribution to surface' enable surface-based selections.
|
| September 2004 | A summary of the science behind YASARA is
available in movie format. (PhD thesis defence, 27th of September,
Radboud University).
|
August
2004
| Structural alignments are handled by SHEBA via a Python plugin
(Linux). New facilities for building small molecules have been added.
|
July 2004
| A 'neutralizing plasma' allows to run Particle Mesh Ewald simulations also with non-neutral simulation cells. Simulation algorithms and energy calculations have been improved and run a bit faster now.
|
June 2004
| The Spaceball 3D controller
is now supported in Linux.
|
May
2004
| YASARA shows all kinds of surfaces, with transparency and updated in real-time. Now you can see the surface adapt while you change torsion angles or run molecular dynamics simulations. Surface environments permit to display and calculate partial surfaces. An interface to the MSMS program allows to display analytic molecular surfaces.
|
April 2004
| YASARA calculates VdW, molecular and solvent accessible surface areas.
|
March 2004
| A plugin for Bert de Groot's CONCOORD program
allows to quickly analyze protein flexibility.
|
February
2004
| YASARA's macro language 'Yanaconda' gets an extreme makeover,
with lots of new functions, better list handling and huge speedups.
|
November 2003
| Adding chemical modifications to small molecules is much easier now.
|
October 2003
| YASARA displays structural alignments and allows to change distances,
angles and dihedrals interactively.
|
| September 2003 |
YASARA is officially launched at the ICMSB 2003. Download your personal edition now!
|
| August 2003 | The YASARA PDBFINDER II plugin
allows you to quickly locate conserved residues and identify the well determined regions in every PDB structure. |
| July 2003 | WHAT IF and YASARA work together in the Twinset |
| June 2003 | YASARA mail orders are now handled by a robotic system. |
| May 2003 | YASARA online shop, automatic order processing. |
| April 2003 | YASARA documentation system. Every change in the program is now reflected automatically in the documentation. |
| March 2003 | You can now write YASARA plugins in Python to add your own functions. |
| February 2003 | Our mascott Yami is born (2003/02/02). First YASARA tutorial written in Yanaconda: Working with Yasara. |
| January 2003 | YASARA displays hydrogen bonds. Internal YASARA beta testing starts at the CMBI. |
| December 2002 | YASARA gets a fully functional macro language
- Yanaconda (Yet ANother Abridged COding'N'Development Approach). |
| November 2002 | Added support for labels and arrows. |
| October 2002 | YASARA can display molecules as balls'n'sticks and now also in true OpenGL quad-buffered stereo. |
| September 2002 | YASARA, WHAT IF and SeqCF-Threader submit predictions for over
40 CASP5 targets. The model for target 168 is ranked first among ~150 submissions. |
| August 2002 | Thanks to Models@Home
, the new YAMBER force fields are ready, just in time for CASP5. |
| July 2002 | A Python-based expert system for protein structure prediction,
to become part of the WHAT IF/YASARA Twinset
. |
| June 2002 | A knowledge-based loop modeler, and a new scoring function for CASP5. |
| May 2002 | YASARA gets an OpenGL based window manager and access to many different file formats thanks to OpenBabel. |
| April 2002 | A new module to predict pKa values, also in protein crystals. |
| March 2002 | YASARA can display three dimensional fonts with depth.
Unlimted undo/redo now available. |
| February 2002 |
YASARA can display molecules as sticks. |
| January 2002 |
YASARA's PVL based Particle Mesh Ewald module finally completed. |
| December 2001 | Development of an object-oriented modeling environment in Python. Will become a plugin for the WHAT IF/YASARA Twinset. |
| November 2001 | Development of a Particle Mesh Ewald (PME) module to calculate long-range electrostatic interactions starts. |
| October 2001 | PVL based molecular dynamics algorithms enable periodic boundaries,
triclinic simulation cells and faster neighbour searches. |
| September 2001 |
New very Fast Fourier Transform (FFT) algorithms using PVL. |
| August 2001 |
Multimedia presentation capabilities using OpenGL texture mapping. |
| July 2001 | New algorithm to display molecules in space-filling mode with OpenGL and PVL,
35x faster than the usual approach. |
| June 2001 | First molecule displayed on screen using OpenGL. |
| May 2001 | YASARA for Linux and Windows gets basic OpenGL support. |
| April 2001 | PVL, the Portable Vector Language, is ready and provides a huge performance boost for YASARA. |
| March 2001 | Using Models@Home
, YASARA performs large scale docking of glycosaminoglycans and proteins. See Proteins
(2003) in press. |
| February 2001 | Using Models@Home, NOVA becomes the first 'self-parameterizing' force field. See
Proteins (2002) 47,393-402. |
| January 2001 |
A new, faster implementation of the AMBER force field.
First version of YASARA for Windows,
console without graphics only. |
| December 2000 | Models@Home, a screen saver to turn idle PCs into a distributed computing cluster
is ready and runs YASARA in parallel. See Bioinformatics (2002) 18
, 315-318 |
| November 2000 | www.YASARA.com goes online. The last version of YASARA for DOS is ready. |
| August 2000 | A "Transgenic Algorithm
" combined with a WHAT IF/ WHAT_CHECK/ GenThreader/ 3DPSSM/ Bioinbgu interface is applied to
8 CASP4 targets (5x homology modeling,
1x fold recognition, 2x ab initio, 5 have been submitted). |
| July 2000 | The currently 26 PCs at the CMBI now form a distributed computing cluster, YASARA gets a parallel job scheduler. |
| June 2000 | YASARA for Linux finally runs in console-mode,
graphics are on their way. |
| March 2000
| YASARA development moves to the Center for Molecular and Biomolecular Informatics
(CMBI) in Nijmegen/Netherlands. |
| December 1999
| A new graphical user interface allows intuitive access to all functions.
|
| December 1998 | Other force fields like AMBER
can be imported. |
| October 1998 |
YASARA becomes parallel using the Molecular Dynamics Network Protocol
MODYNP. |
| September 1998 | Photorealistic molecule images can be created thanks to a
POVRay interface. |
| June 1998 | "Potentials of mean force" have been added to allow true fold prediction.
|
| April 1998 | The
"Virtual Ribosome" to fold proteins based on
NMR NOE restraints is ready. |
| January 1998 | Protein/DNA docking module. |
| November 1997 |
YASARA NOVA Force Field with off-center point charges ready,
first interactive real-time simulation on screen of a Pentium 133 (32 MB ram):
1ACP, 768 atoms, space filling, quad-buffered stereo, 12 frames per second. |
| August 1997 | The molecule rendering engine triples its speed thanks to the
1st generation YAMAC (YASARA Molecule Accelerator, a directly programmed Tseng ET6000 graphics board). |
| May 1997 | YASARA reads PDB files. |
| October 1996 |
Support for a Virtual Reality Headset
including motion-tracking. |
| September 1996 | Development of the space-fill molecule rendering engine starts. |
| July 1996 | YASARA gets support for 3D shutter glasses. |
| Autumn 1993 | After some early "molecular graphics" attempts on a
1MIPS machine, the first line of YASARA source code is written on an Intel 386SX/20MHz,
2MB ram, MS-DOS. |
