||A completely revamped YASARA for MacOS is out: 64bit, support for Retina displays, touch
gestures on the MacBook trackpad, faster MD simulations.
||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.
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
||YASARA supports the NMR
Exchange Format (NEF) for reading and writing restraints.
||YASARA can automatically
write scientific reports including tables, plots and
figures, for example about
molecular dynamics simulations.
module developed by Chris Spronk links ARIA and YASARA
to fully automatically determine NMR structures from their
||An interactive small molecule
builder is available, watch
the movie here.
||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.
|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.
|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%.
|YASARA's NMR module supports
residual dipolar couplings (RDCs).
|Batch-processing of large
data sets is now possible from the GUI, without having to
write a macro to loop over the data.
3DM protein superfamily data integration platform has
become a widely used, indispensable tool for protein
analysis and now includes DNA diagnostics
|A 64-bit version of YASARA
for Windows is available
|The YASARA Structure/WHAT IF
Twinset is available for Windows 64-bit
|Several new force fields
are available: AMBER10, AMBER11 (known as ff99sb*-ILDN),
AMBER14 and AMBER14IPQ. Included are GLYCAM06 for
Lipid14 for phospholipids and lots of new ion parameters by
|A 64-bit version of YASARA
for Linux is available, so that you don't need to install
libraries for backwards compatibility, and memory limits
will no longer
impair your MD simulation of the ribosome.
|To prepare for the coming
replacement of classic PDB files with the new PDBx files,
includes a fast and reliable interface to mmCIF/PDBx and CIF
allowing to load the new giant structures like 4V8P that are
available in mmCIF format
|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.
internal data structures were redesigned, many operations
significantly faster. YASARA supports 4-character
(as required by the new PDBx/mmCIF format) and up to 7
per atom. The *.sce and *.yob file formats require less
space on disk
supports GPUs from
AMD, nVIDIA and Intel to accelerate molecular dynamics
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
|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
reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8
|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.
|YASARA supports pair lists,
which can be updated every Nth step. With N=10, simulations
run 74% faster.
|YASARA supports the AVX2
vector instruction set, introduced with the Intel Haswell
CPU architecture in summer 2013.
|YASARA features a new mixed
multiple timestep algorithm, which allows to reach a 5 fs
timestep during MD simulations.
|YASARA supports the FMA3
vector instruction set for 'fused multiply add operations',
with the AMD Piledriver CPU architecture in summer 2012.
|YASARA supports the AVX
vector instruction set, introduced with the Intel Sandy
architecture in spring 2011 and AMD Bulldozer CPU
|YASARA's graphics engine
receives a major update to make optimal use of new OpenGL
and multiple CPU cores. Drawing runs 300-450% faster,
depending on CPU
and GPU type.
first 'YASARA tablets' are shipped to our customers.
Molecular modeling and simulations at your fingertips for
for Android is released,
providing today's most feature complete molecular modeling
smartphones and tablets, including interactive MD
|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.
VINA has been
seamlessly integrated into YASARA, allowing to dock
with just four
mouse clicks, many thanks to Scripps Research Institute.
allows to keep selected side-chains flexible during docking,
addition to the previous approach of docking against a
ensemble with alternative high-scoring side-chain rotamers.
module includes a new hybridization algorithm to
combine the best parts
of models built from different templates and/or with
module features a new database of 'P'rofiles from
'S'tructurally related 'P'roteins (PSSP), which provides
profiles for each template in the PDB, resulting in more
|YASARA includes modeling
functions to transfer and replicate structure fragments,
|YASARA includes functionality
to analyze and visualize hydrophobic,
pi-pi and cation-pi interactions,
also as part of the ligand explorer.
|YASARA performs 'twisted structural alignments',
i.e. it bends and winds proteins to maximize the number of
aligned residues, for example to create sequence profiles
|YASARA can extrude 3D objects from simple 2D bitmaps,
which makes it easy to create 3D animations without having
to build 3D objects first.
|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.
|YASARA includes a much
faster and more accurate relaunch of the NOVA force field
Optimization in VAcuo with automatic force field parameter
for organic molecules.
|YASARA's built-in BLAST
supports two new databases: UniRef90 and PDBC, the PDB
sequences extracted from the coordinate section, which is
than the usual SEQRES data. Redundant sequences are sorted
|YASARA macros, plugins and
scripts can freely define user interfaces to create their
windows whenever needed. Now every user can easily add
functionality to YASARA.
|YASARA can create user
interfaces in secondary windows, for example on a touch
makes it easy for the unexperienced audience at expositions
etc. to get
in touch with molecular modeling, as shown in this YouTube movie.
(dynamic cross-correlation matrix) can be calculated
from MD simulations and visualized.
|A new structural alignment
ligands by indentifying common structural motifs.
|YASARA features GPU
accelerated high-quality anaglyph stereo mode that tricks
brain into seeing full color and enables stereo everywhere,
notebooks. Every order is now shipped with red/cyan glasses.
creates better alignments using sequence profiles, that can
be augmented with structure- based profiles of related
|YASARA supports spherical sky
projections that are mirrored
in protein secondary structure etc.
|YASARA includes a new
selection mechanism, that permits to interactively
select atoms within a rectangular box, an arbitrary
area or a 3D sphere.
|A secondary structure
morpher has been developed, which allows to seamlessly
between realistic (close to Calphas) and idealistic
strands and helices) secondary structure.
purchased a license of David Jones' PsiPred program, which
more accurate secondary structure prediction, for example
|YASARA's graphics engine
makes full use of the ever increasing GPU power by providing
shading (OpenGL 2.X) and hardware tessellation (OpenGL
where the GPU increases the geometric details of the polygon
Contributed by Jacobus van Meel.
|Docking with receptor
flexibility is supported by creating an ensemble of receptor
with alternative high-scoring solutions of the side-chain
|The secondary structure
display has been improved heavily, lots of new options
configure every aspect (e.g. rectangular, elliptical or
|A stochastic rotamer
alternative high scoring side-chain packings to capture
|Dynamically updated or static
& plastic wire frames can
be displayed for all kinds of polygon meshes like surfaces.
|Full-scene antialiasing is
available to avoid jagged polygon edges, contributed by
Jacobus van Meel.
|YASARA includes an interface to the
FoldX program for free energy calculations,
contributed by Joost van Durme.
|YASARA provides identification, analysis and visualization
of internal cavities.
|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
dynamics algorithms have been rewritten and are now the
For a typical protein simulation in explicit solvent, they
3.2× (1 CPU core) and 4.3× (8 CPU cores) as fast as
previously, and require significantly less memory.
simulations of membrane proteins fully automatically, at
of a button. This includes identification of the
region, embedding and equilibration.
|YASARA supports interlaced
stereo for a new generation of screens like the Zalman
allowing to build a molecular
cave for just 250 EUR.
includes a customized version of APBS
to solve the Poisson-Boltzmann equation, adding an
method to calculate electrostatic potentials and solvation
|Several new graphics
styles to visualize electrostatic potentials are
multiple interactive cut-planes to look inside
and other objects.
force fields deliver the most accurate
MD simulations and win five CASP8
Yanaconda macro language runs up to 150× faster and features
oligosaccharide builder with
stepwise energy-minimization has been released.
|After five years of
development, the final YASARA stage 'YASARA
Structure' has just been released with YASARA version
are welcome to join the festive activities by clicking Help
help movie > Triple 8 celebration day.
|Two new force fields are
available: The YASARA force
has been derived from YAMBER3 by adding knowledge-based
potentials (one-, two- and three-dimensional), and the
YASARA2 force field, which
knowledge based 1D and 3D packing potentials.
|YASARA performs a
new kind of force field based structure
validation that works also for ligands, supporting 11
|The NMR module to perform
NMR structure determination has been released.
|A built-in (PSI-)BLAST is
available, local sequence databases (PDB,SwissProt,TrEMBL)
automatically and augmented with
validation data to identify the best PDB structure for a
Side-Chains With a Rotamer Library and very fast dead-end
using the SCWRL3 algorithm. Additional
considers electrostatic and packing interaction, as well
|The 'Docking experiment'
performs small molecule docking using
version of AutoDock.
|YASARA contains a new pH
dependent hydrogen bonding network optimizer
that fully considers ligands.
experiment' takes all the
steps from a
target FASTA sequence to a fully refined homology model
a scientific report about the
|YASARA contains a knowledge-based
loop modeler and optimizer.
|YASARA performs secondary
side-by-side stereo for flat-screens that do not work with
scene content browser with context menus
in the top right head-up display allows to easily and
and modify the scene.
|YASARA has a new Python
interface: stand-alone Python scripts can simply import the
Python module and directly use all YASARA functions.
|YASARA supports multiple
structural alignments using Arun Konagurthu's MUSTANG
has been fully incorporated.
|YASARA performs local
Smith&Waterman and global Needleman&Wunsch sequence
and can use them to superpose structures.
contributes the THESEUS maximum likelihood algorithm to
bundles of NMR structures fully automatically, putting more
the structurally conserved regions.
|YASARA features a new
multi-threaded high-speed algorithm to draw molecular
like Van der Waals and solvent accessible surfaces, they now
real-time to moving atoms.
is now available for MacOS, including special support
Mouse and MacBook track pad.
|YASARA's OpenGL graphics
engine supports real-time shadows
lighting, even on old notebooks that do not have
shaders (OpenGL 1.2).
|YASARA gets a newly
styled look that also adapts to your current
|YASARA now supports parallel
molecular dynamics simulations on
|The new YAMBER3 force
field is available, providing more accurate molecular
|YASARA can calculate force
field energies individually per unit (atom, residue,
to locate regions of interest.
|YASARA uses eigenvector
analysis to calculate angles and dihedrals between groups of
helices or planar side-chains.
algorithm provides fully
automatic force field parameter assignment for organic
unusual amino acids or ligands. 98% of the PDB can now be
the touch of a button.
|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
|Structure based alignments
are now available in Windows and Linux using the methods CE,
and Sheba thanks to a web server plugin developed by
and Mikael Roche at IBCP Lyon/France.
|Molecular graphics can be
augmented with all kinds of solid objects: spheres,
ellipsoids, cubes, boxes, cylinders, cones, prisms and
|YASARA now includes a
SMILES based library of chemical knowledge about pH
orders and protonation patterns, making it possible to type
add missing hydrogens to any organic molecule at any pH from
0 to 14.
|YASARA imports OpenOffice
Impress and Microsoft PowerPoint presentations and makes it
easy to add
|YASARA calculates Van der
Waals, molecular and solvent accessible volumes
|The YASARA/WHATIF Twinset
adds structural alignments, a hydrogen bonding network
regularizer for covalent geometry and the option to analyze
dependent rotamer distributions.
|The YASARA/WHATIF Twinset
is released. YASARA can now perform 20+ different
angles, torsions, omega angle, Ramachandran plot, side-chain
proline rings, chirality, planarity, backbone conformation,
peptide-plane flips, bumps, 3D packing quality,
distribution, unsatisfied H-bonds, or flipped Asn/Gln/His
|YASARA encodes MPEG movies
from normal or ray-traced screenshots. Can be pasted into
|A fast implicit solvent
model using a first order boundary element approach allows
|A flexible implementation
of multi-dimensional tables including visualization makes
all kinds of
data analysis very easy.
|Heavily improved surface
analysis becomes available. The 'FirstSurf' command allows
surfaces, the new operators 'with distance from surface' and
contribution to surface' enable surface-based selections.
||A summary of the science
behind YASARA is available in
(PhD thesis defence, 27th of September, Radboud University).
|Structural alignments are
handled by SHEBA via a Python plugin (Linux). New facilities
for building small molecules have been
'neutralizing plasma' allows to run
Particle Mesh Ewald simulations also with non-neutral
Simulation algorithms and energy calculations have been
run a bit faster now.
3D controller is now
supported in Linux.
|YASARA shows all kinds of surfaces, with transparency and
real-time. Now you can see the surface adapt while you
angles or run molecular dynamics simulations. Surface
permit to display and calculate partial surfaces. An
interface to the
MSMS program allows to display analytic molecular surfaces.
|YASARA calculates VdW,
molecular and solvent accessible surface areas.
Bert de Groot's CONCOORD program allows to quickly
|YASARA's macro language
'Yanaconda' gets an extreme makeover, with lots of new
better list handling and huge speedups.
modifications to small molecules is much easier now.
|YASARA displays structural
alignments and allows to change distances, angles and
||YASARA is officially launched at the ICMSB 2003. Download
your personal edition now!
||The YASARA PDBFINDER II plugin
allows you to quickly locate conserved residues and identify
determined regions in every PDB structure.
||WHAT IF and YASARA work together in the Twinset
||YASARA mail orders are now handled by a robotic system.
||YASARA online shop, automatic order processing.
||YASARA documentation system. Every change in the
program is now reflected automatically in the documentation.
||You can now write YASARA plugins in Python to add your
||Our mascott Yami is born (2003/02/02). First YASARA
tutorial written in Yanaconda: Working with Yasara.
||YASARA displays hydrogen bonds. Internal YASARA beta
testing starts at the CMBI.
||YASARA gets a fully functional macro language -
Yanaconda (Yet ANother Abridged COding'N'Development
||Added support for labels and arrows.
||YASARA can display molecules as balls'n'sticks and now
also in true OpenGL quad-buffered stereo.
||YASARA, WHAT IF and SeqCF-Threader submit predictions
for over 40 CASP5 targets. The model for target 168 is
among ~150 submissions.
||Thanks to Models@Home , the
new YAMBER force fields are ready, just in time for CASP5.
||A Python-based expert system for protein structure
prediction, to become part of the WHAT
||A knowledge-based loop modeler, and a new scoring
function for CASP5.
||YASARA gets an OpenGL based window manager and access
to many different file formats thanks to OpenBabel.
||A new module to predict pKa values, also in protein
||YASARA can display three dimensional fonts with depth.
Unlimited undo/redo now available.
||YASARA can display molecules as sticks.
||YASARA's PVL based Particle Mesh Ewald module finally
||Development of an object-oriented modeling environment
in Python. Will become a plugin for the WHAT IF/YASARA
||Development of a Particle Mesh Ewald (PME) module to
calculate long-range electrostatic interactions starts.
||PVL based molecular dynamics algorithms enable periodic
boundaries, triclinic simulation cells and faster neighbour
||New very Fast Fourier Transform (FFT) algorithms using
||Multimedia presentation capabilities using OpenGL
||New algorithm to display molecules in space-filling
mode with OpenGL and PVL, 35× faster than the usual
||First molecule displayed on screen using OpenGL.
||YASARA for Linux and Windows gets basic OpenGL support.
||PVL, the Portable Vector Language, is ready and
provides a huge performance boost for YASARA.
||Using Models@Home , YASARA
performs large scale docking of glycosaminoglycans and
proteins. See Proteins
(2003) in press.
||Using Models@Home, NOVA
becomes the first 'self-parameterizing' force field. See Proteins
||A new, faster implementation of the AMBER force field.
First version of YASARA for Windows, console without
||Models@Home, a screen saver to
turn idle PCs into a distributed computing cluster is
runs YASARA in parallel. See Bioinformatics (2002) 18
||www.YASARA.com goes online. The last version of YASARA
for DOS is ready.
||A "Transgenic Algorithm" combined
with a WHAT IF/ WHAT_CHECK/ GenThreader/ 3DPSSM/ Bioinbgu
applied to 8 CASP4 targets (5x
homology modeling, 1× fold recognition,
2× ab initio, 5 have been submitted).
||The currently 26 PCs at the CMBI
now form a distributed computing cluster, YASARA gets
||YASARA for Linux finally runs in console-mode, graphics
are on their way.
||YASARA development moves to the Center
for Molecular and Biomolecular
Informatics (CMBI) in Nijmegen/Netherlands.
||A new graphical user interface allows intuitive access to
||Other force fields like AMBER
can be imported.
||YASARA becomes parallel using the Molecular Dynamics
Network Protocol MODYNP.
||Photorealistic molecule images can be
created thanks to a POVRay
||Potentials of mean force have been added to allow true
||The "Virtual Ribosome" to fold proteins based on NMR NOE
restraints is ready.
||Protein/DNA docking module.
||YASARA NOVA Force Field with
off-center point charges ready, first interactive real-time
on screen of a Pentium 133 (32 MB RAM): 1ACP, 768 atoms,
quad-buffered stereo, 12 frames per second.
||The molecule rendering engine triples its speed thanks
to the 1st generation YAMAC (YASARA Molecule Accelerator, a
programmed Tseng ET6000 graphics board).
||YASARA reads PDB files.
||Support for a Virtual
Headset including motion-tracking.
||Development of the space-fill molecule rendering engine
||YASARA gets support for 3D shutter glasses.
||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.