January 2017
|
YASARA's graphics engine
and user interface have been reimplemented for high and ultra-high
resolutions, up to 4K in YASARA View (3840×2160 pixels) and 8K in
YASARA Model+ (7680×4320 pixels).
|
December 2016
|
MD simulations run 10-20% faster thanks to support for dodecahedral simulation cells, which reduce the number of unnecessarily simulated water molecules by about 50%.
|
November 2016
|
YASARA's NMR module supports residual dipolar couplings (RDCs).
|
September 2016
|
Batch-processing of large data sets is now possible from the GUI, without having to write a macro to loop over the data.
|
August 2016
|
The Bio-Prodict 3DM protein superfamily data integration platform has become a widely used, indispensable tool for protein analysis and now includes DNA diagnostics
|
June 2016
|
A 64-bit version of YASARA
for Windows is available |
April 2016
|
The YASARA Structure/WHAT IF Twinset is available for Windows 64-bit
|
February 2016
|
Several new force fields
are available: AMBER10, AMBER11 (known as ff99sb*-ILDN), AMBER12,
AMBER14 and AMBER14IPQ. Included are GLYCAM06 for carbohydrates,
Lipid14 for phospholipids and lots of new ion parameters by Li&Merz.
|
October 2015
|
A 64-bit version of YASARA
for Linux is available, so that you don't need to install extra
libraries for backwards compatibility, and memory limits will no longer
impair your MD simulation of the ribosome.
|
August 2015
|
To prepare for the coming
replacement of classic PDB files with the new PDBx files, YASARA
includes a fast and reliable interface to mmCIF/PDBx and CIF files,
allowing to load the new giant structures like 4V8P that are only
available in mmCIF format
|
June 2015
|
YASARA allows to create alternative views of the scene, each with its own styles,
visibilites, surfaces, arrows etc. Tabs at the top allow to quickly change between the views. |
May 2015
|
YASARA's
internal data structures were redesigned, many operations run
significantly faster. YASARA supports 4-character chain/molecule names
(as required by the new PDBx/mmCIF format) and up to 7 covalent bonds
per atom. The *.sce and *.yob file formats require less space on disk |
March 2015
|
YASARA supports GPUs from
AMD, nVIDIA and Intel to accelerate molecular dynamics simulations,
boosting the DHFR benchmark to 253 ns/day (Core i7-5960X with Geforce GTX 980, PME, 8.0 A VdW cutoff, correct atom masses,
reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX
registers). |
December 2014
|
Thanks to another round of
algorithmic improvements, the DHFR benchmark now runs with 160 ns/day
on a Core i7-5960X (no GPU, PME, 8.0 A VdW cutoff, correct atom masses,
reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX
registers).
|
May 2014
|
YASARA's MD algorithms
have been largely rewritten to boost performance. On an Intel Core i7
4770, this YASARA now reaches 81ns/day in the DHFR benchmark, which is
almost 3× as fast as previous YASARA versions.
|
March 2014
|
YASARA supports pair lists, which can be updated every Nth step. With N=10, simulations run 74% faster.
|
January 2014
|
YASARA supports the AVX2 vector instruction set, introduced with the Intel Haswell CPU architecture in summer 2013.
|
November 2013
|
YASARA features a new mixed multiple timestep algorithm, which allows to reach a 5 fs timestep during MD simulations.
|
October 2013
|
YASARA supports the FMA3
vector instruction set for 'fused multiply add operations', introduced
with the AMD Piledriver CPU architecture in summer 2012.
|
September 2013
|
YASARA supports the AVX
vector instruction set, introduced with the Intel Sandy Bridge CPU
architecture in spring 2011 and AMD Bulldozer CPU architecture in
autumn 2011.
|
June 2013
|
YASARA's graphics engine
receives a major update to make optimal use of new OpenGL functionality
and multiple CPU cores. Drawing runs 300-450% faster, depending on CPU
and GPU type.
|
April 2013
|
The first 'YASARA tablets' are shipped to our customers. Molecular modeling and simulations at your fingertips for 199 EUR.
|
March 2013
|
YASARA for Android is released,
providing today's most feature complete molecular modeling software on
smartphones and tablets, including interactive MD simulations.
|
February 2013
|
A touchable YASARA is released, which supports multi-touch gestures and provides a customized on-screen keyboard. The first supported devices are Windows 8 tablets.
|
January 2013
|
AutoDock VINA has been
seamlessly integrated into YASARA, allowing to dock with just four
mouse clicks, many thanks to Scripps Research Institute.
|
December 2012
|
YASARA's docking module
allows to keep selected side-chains flexible during docking, in
addition to the previous approach of docking against a receptor
ensemble with alternative high-scoring side-chain rotamers.
|
November 2012
|
YASARA's homology modeling
module includes a new hybridization algorithm to combine the best parts
of models built from different templates and/or with different
alignments.
|
September 2012
|
YASARA's homology modeling
module features a new database of 'P'rofiles from 'S'equence and
'S'tructurally related 'P'roteins (PSSP), which provides precalculated
profiles for each template in the PDB, resulting in more accurate
alignments.
|
August 2012
|
YASARA includes modeling functions to transfer and replicate structure fragments, e.g. loops or entire domains.
|
July 2012
|
YASARA includes functionality to analyze and visualize hydrophobic, pi-pi and cation-pi interactions, also as part of the ligand explorer.
|
June 2012
|
YASARA performs 'twisted structural alignments',
i.e. it bends and winds proteins to maximize the number of structurally
aligned residues, for example to create sequence profiles for homology
modeling.
|
April 2012
|
YASARA can extrude 3D objects from simple 2D bitmaps, which makes it easy to create 3D animations without having to build 3D objects first.
|
February 2012
|
The new functions
'Inflate' and 'Deflate' generate 3D molecule coordinates from
nonsense,1D or 2D coordinates, and convert them back to a flat 2D
structure, which can be styled like a structural formula.
|
January 2012
|
YASARA includes a much
faster and more accurate relaunch of the NOVA force field for proteiN
Optimization in VAcuo with automatic force field parameter assignment
for organic molecules.
|
December 2011
|
YASARA's built-in BLAST
supports two new databases: UniRef90 and PDBC, the PDB protein
sequences extracted from the coordinate section, which is more useful
than the usual SEQRES data. Redundant sequences are sorted by structure
quality.
|
October 2011
|
YASARA macros, plugins and
scripts can freely define user interfaces to create their own custom
windows whenever needed. Now every user can easily add custom
functionality to YASARA.
|
May 2011
|
YASARA can create user
interfaces in secondary windows, for example on a touch screen. This
makes it easy for the unexperienced audience at expositions etc. to get
in touch with molecular modeling, as shown in this YouTube movie.
|
April 2011
|
The DCCM (dynamic cross-correlation matrix) can be calculated from MD simulations and visualized.
|
March 2011
|
A new structural alignment algorithm matches ligands by indentifying common structural motifs.
|
Feburary 2011
|
YASARA features GPU
accelerated high-quality anaglyph stereo mode that tricks the human
brain into seeing full color and enables stereo everywhere, also on
notebooks. Every order is now shipped with red/cyan glasses.
|
January 2011
|
The homology modeling experiment
creates better alignments using sequence profiles, that can optionally
be augmented with structure- based profiles of related template
structures.
|
December 2010
|
YASARA supports spherical sky projections that are mirrored in protein secondary structure etc.
|
November 2010
|
YASARA includes a new selection mechanism, that permits to interactively select atoms within a rectangular box, an arbitrary area or a 3D sphere.
|
October 2010
|
A secondary structure
morpher has been developed, which allows to seamlessly interpolate
between realistic (close to Calphas) and idealistic (perfectly straight
strands and helices) secondary structure.
|
September 2010
|
YASARA Biosciences
purchased a license of David Jones' PsiPred program, which now provides
more accurate secondary structure prediction, for example during
homology modeling.
|
August 2010
|
YASARA's graphics engine
makes full use of the ever increasing GPU power by providing phong
shading (OpenGL 2.X) and hardware tessellation (OpenGL 3.X),
where the GPU increases the geometric details of the polygon meshes.
Contributed by Jacobus van Meel.
|
July 2010
|
Docking with receptor
flexibility is supported by creating an ensemble of receptor structures
with alternative high-scoring solutions of the side-chain rotamer
network.
|
June 2010
|
The secondary structure
display has been improved heavily, lots of new options permit to
configure every aspect (e.g. rectangular, elliptical or barbell-like
helix-ribbon cross-sections).
|
May 2010
|
A stochastic rotamer optimizer generates alternative high scoring side-chain packings to capture conformational freedom.
|
April 2010
|
Dynamically updated or static & plastic wire frames can be displayed for all kinds of polygon meshes like surfaces.
|
March 2010
|
Full-scene antialiasing is available to avoid jagged polygon edges, contributed by Jacobus van Meel.
|
February 2010
|
YASARA includes an interface to the FoldX program for free energy calculations, contributed by Joost van Durme.
|
December 2009
|
YASARA provides identification, analysis and visualization of internal cavities.
|
October 2009
|
YASARA can constrain bond
lengths using the LINCS algorithm to enable
larger timesteps. Combined with the new MD
algorithms simulations now run
between 4.1× (1 CPU core) and 5.2× (8 CPU cores) as fast as
previously. |
September 2009
|
YASARA's
molecular dynamics algorithms have been rewritten and are now the
fastest around.
For a typical protein simulation in explicit solvent, they run between
3.2× (1 CPU core) and 4.3× (8 CPU cores) as fast as
previously, and require significantly less memory.
|
August 2009
|
YASARA
runs simulations of membrane proteins fully automatically, at the touch
of a button. This includes identification of the transmembrane
region, embedding and equilibration.
|
June 2009
|
YASARA supports interlaced
stereo for a new generation of screens like the Zalman ZM-M220W,
allowing to build a molecular modeling
cave for just 250 EUR.
|
March 2009
|
YASARA includes a customized version of APBS
to solve the Poisson-Boltzmann equation, adding an additional
method to calculate electrostatic potentials and solvation energies.
|
February 2009
|
Several new graphics
styles to visualize electrostatic potentials are available.
|
January 2009
|
YASARA
supports multiple interactive cut-planes to look inside surfaces
and other objects.
|
December 2008
|
YASARA's new force fields deliver the most accurate
MD simulations and win five CASP8 targets.
|
November 2008
|
YASARA's built-in
Yanaconda macro language runs up to 150× faster and features
vector processing.
|
October 2008
|
An interactive oligosaccharide builder with
stepwise energy-minimization has been released.
|
August 2008
|
After five years of
development, the final YASARA stage 'YASARA
Structure' has just been released with YASARA version 8.8.8. You
are welcome to join the festive activities by clicking Help > Play
help movie > Triple 8 celebration day.
|
August 2008
|
Two new force fields are
available: The YASARA force field, which
has been derived from YAMBER3 by adding knowledge-based dihedral
potentials (one-, two- and three-dimensional), and the YASARA2 force field, which contains additional
knowledge based 1D and 3D packing potentials.
|
August 2008
|
YASARA performs a new kind of force field based structure
validation that works also for ligands, supporting 11 different
checks.
|
August 2008
|
The NMR module to perform NMR structure determination has been released.
|
August 2008
|
A built-in (PSI-)BLAST is
available, local sequence databases (PDB,SwissProt,TrEMBL) are updated
automatically and augmented with additional
validation data to identify the best PDB structure for a given sequence.
|
August 2008
|
YASARA optimizes
Side-Chains With a Rotamer Library and very fast dead-end elimination
using the SCWRL3 algorithm. Additional tuning
considers electrostatic and packing interaction, as well as solvation
effects.
|
July 2008
|
The 'Docking experiment'
performs small molecule docking using a tuned
version of AutoDock.
|
June 2008
|
YASARA contains a new pH dependent hydrogen bonding network optimizer
that fully considers ligands.
|
May 2008
|
The 'HomologyModeling
experiment' takes all the steps from a
target FASTA sequence to a fully refined homology model and writes
a scientific report about the modeling
|
April 2008
|
YASARA contains a knowledge-based loop modeler and optimizer.
|
March 2008
|
YASARA performs secondary
structure prediction.
|
February 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.
Unlimited 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, 35× 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
(5× homology modeling, 1× fold recognition,
2× 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. |
