September 2023 |
YASARA has been ported to ARM 64bit CPUs with Neon SIMD
instruction set. The first supported operating system is
MacOS, where the CPU-only DHFR molecular dynamics benchmark
running on an Apple MacBook Air from 2020 with 4 performance
and 4 efficiency cores jumps from 75
ns/day (using Rosetta-2 emulation) to 125 ns/day (using
the new native ARM Neon code). |
April 2023 |
Virtual reality is here on Linux
and Windows PCs, allowing a seamless switch between a
comfortable seated and an exciting standing environment. Watch the introductory movie here. |
August 2022 |
YASARA displays electron
densities and other maps in six different styles. |
February 2022 |
The PetWorld
database, a collection of gigastructures for interactive
exploration has been released at www.PetWorld.vision.
Contribute your own models and get all YASARA stages free of
charge. |
January 2022 |
YASARA can build entire genomes
(single- and double-stranded DNA or RNA), taking as input
the FASTA sequence and a collection of nucleic acid
binding proteins. Proteins are attached automatically
to their binding sites. |
December 2021 |
The new facilities for building gigastructures have
been used to construct a SARS-CoV-2 model which can be
explored interactively. |
November 2021 |
YASARA can shrink molecules to
a coarse-grained representation made of "pet atoms".This
reduces the atom count by about a factor of 50 and speeds
up construction and MD simulations of giant systems. |
October 2021 |
A new
packing engine to build gigastructures with billions of
atoms is available. Compartments can be defined with
polygon meshes and filled with proteins inside, outside and
on the boundary (in this case usually including membrane
fragments). The packing can be done using pet atoms (see
above) to complete the task quickly. |
August 2021 |
YASARA includes the OpenH264 MPEG4 encoder to save high
quality movies with high compression. |
June 2021 |
YASARA's Vulkan graphics engine has been improved to calculate
per-pixel ambient lighting, yielding a better 3D
appearance. |
December 2020 |
YASARA enters the billion atom world. Identical copies of
object (instances) can be created for visualization, while
the number of atoms in the soup remains unchanged. The new
Vulkan/Metal graphics engine can display these instances so
quickly that interactive visualization
of systems with billions of atoms in all common styles
from balls and sticks to ribbons is now possible. |
October 2020 |
YASARA calculates and shows contact
surfaces, the help movie 'Surfaces II' has been updated to
include the new, easier approach |
July 2020 |
After nearly 30 years of service, OpenGL has reached the
end of its lifetime as the top API for cross-platform 3D
graphics. Its successor is called Vulkan and delivers more
performance, control and flexibility. The YASARA
graphics engine has been rewritten from scratch for Vulkan
and now delivers in real-time what you previously only got
from POVRay via slow ray-tracing (e.g. contact hardening
soft shadows for improved depth perception). In MacOS,
YASARA now uses the Metal API, since OpenGL is deprecated
there. |
April 2019 |
The much faster OpenGL graphics engine that made the Android
Virtual Reality Workstation possible is now available
for Linux, MacOS and Windows. Especially the display of
balls, ball&sticks and sticks now runs 2-3× as fast as
previously. |
January 2019 |
YASARA supports docking of covalently bound ligands using
AutoDock's flexible side-chain
approach. |
November 2018 |
A completely revamped YASARA for MacOS is out: 64bit, support for Retina displays, touch
gestures on the MacBook trackpad, faster MD simulations. |
July 2018 |
An extensively tested 3D cinema setup is available for
Linux and Windows 1200 EUR: The
Optoma UHD40 beamer, that delivers 3D for DLP-link glasses
with 1920×1080 pixels, and 4K (3840*2160 pixels) in 2D. |
April 2018 |
The
YASARA Virtual Reality Workstation is on sale for 175 EUR.
You can now do interactive modeling and simulation in 3D
with head-tracking and without cables anywhere on the
planet. |
February 2018 |
YASARA supports the NMR
Exchange Format (NEF) for reading and writing restraints. |
December 2017 |
YASARA can automatically
write scientific reports including tables, plots and
figures, for example about
molecular dynamics simulations. |
August 2017 |
The YARIA
module developed by Chris Spronk links ARIA and YASARA
to fully automatically determine NMR structures from their
spectra. |
June 2017 |
An interactive small molecule
builder is available, watch
the movie here. |
April 2017 |
YASARA's force fields have
been updated. Small molecules are simulated with the new
GAFF2 force field, the new AMBER15IPQ force field is
available, AMBER14 includes the OL15 DNA fine-tuning,
LIPID14 includes cholesterol. Contributed by AMBERTools16. |
February 2017
|
YASARA's graphics engine and
user interface have been reimplemented for high and
ultra-high resolution displays, now supporting video walls
with up to 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 MacOS, 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 (5x
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. |