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
||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.
||The new facilities for building gigastructures have
been used to construct a SARS-CoV-2 model which can be
||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.
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.
||YASARA includes the OpenH264 MPEG4 encoder to save high
quality movies with high compression.
||YASARA's Vulkan graphics engine has been improved to calculate
per-pixel ambient lighting, yielding a better 3D
||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.
||YASARA calculates and shows contact
surfaces, the help movie 'Surfaces II' has been updated to
include the new, easier approach
||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
||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
||YASARA supports docking of covalently bound ligands using
AutoDock's flexible side-chain
||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),
AMBER12, AMBER14 and AMBER14IPQ. Included are GLYCAM06 for
carbohydrates, Lipid14 for phospholipids and lots of new ion
parameters by Li&Merz.
|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
|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
|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.
|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
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
|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
|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',
introduced with the AMD Piledriver CPU architecture in
|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.
|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.
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 software on smartphones
and tablets, including interactive MD simulations.
|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.
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.
homology modeling module includes a new hybridization
algorithm to combine the best parts of models built from
different templates and/or with different alignments.
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
|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
structurally aligned residues, for example to create
sequence profiles for homology modeling.
|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
|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.
|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.
|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.
|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.
(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
the human brain into seeing full color and enables stereo
everywhere, also on notebooks. Every order is now shipped
with red/cyan glasses.
modeling experiment creates better alignments using
sequence profiles, that can optionally be augmented with
structure- based profiles of related template structures.
|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 interpolate
between realistic (close to Calphas) and idealistic
(perfectly straight strands and helices) secondary
|YASARA Biosciences purchased
a license of David Jones' PsiPred program, which now
provides more accurate secondary structure prediction, for
example during homology modeling.
|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.
|Docking with receptor
flexibility is supported by creating an ensemble of receptor
structures with alternative high-scoring solutions of the
side-chain rotamer network.
|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).
|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 as previously.
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.
simulations of membrane proteins fully automatically, at
the touch of a button. This includes identification of
the transmembrane region, embedding and equilibration.
|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.
includes a customized version of APBS to solve the
Poisson-Boltzmann equation, adding an additional
method to calculate electrostatic potentials and solvation
|Several new graphics styles
to visualize electrostatic potentials are
multiple interactive cut-planes to look inside
surfaces and other objects.
force fields deliver the most accurate MD simulations
and win five CASP8 targets.
|YASARA's built-in Yanaconda
macro language runs up to 150× faster and features vector
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
8.8.8. You are welcome to join the festive activities by
clicking Help > Play help movie > Triple 8 celebration
|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.
|YASARA performs a
new kind of force field based structure validation that
works also for ligands, supporting 11 different
|The NMR module to perform
NMR structure determination has been released.
|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.
|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.
|The 'Docking experiment'
performs small molecule docking using
a tuned version of AutoDock.
|YASARA contains a new pH
dependent hydrogen bonding network optimizer that fully
experiment' takes all the
steps from a target FASTA sequence to a fully refined
homology model and writes a scientific
report about the modeling
|YASARA contains a knowledge-based
loop modeler and optimizer.
|YASARA performs secondary
|YASARA supports side-by-side
stereo for flat-screens that do not work with shutter
|A scene content browser with
context menus in the top right head-up display allows to
easily and quickly navigate and modify the scene.
|YASARA has a new Python
interface: stand-alone Python scripts can simply import the
new YASARA Python module and directly use all YASARA
|YASARA supports multiple
structural alignments using Arun Konagurthu's MUSTANG
program, which has been fully incorporated.
|YASARA performs local
Smith&Waterman and global Needleman&Wunsch sequence
alignments and can use them to superpose structures.
|Douglas Theobald contributes
the THESEUS maximum likelihood algorithm to superpose
bundles of NMR structures fully automatically, putting more
emphasis on the structurally conserved regions.
|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.
is now available for MacOS, including special support
for Mighty Mouse and MacBook track pad.
|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).
|YASARA gets a newly
styled look that also adapts to your current operating
|YASARA now supports parallel
molecular dynamics simulations on multiple CPUs.
|The new YAMBER3 force field
is available, providing more accurate molecular dynamics
|YASARA can calculate force
field energies individually per unit (atom, residue,
molecule, object) to locate regions of interest.
|YASARA uses eigenvector
analysis to calculate angles and dihedrals between groups of
atoms like helices or planar side-chains.
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.
|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,
Multiprot and Sheba thanks to a web server plugin developed
by Emmanuel Bettler 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 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.
|YASARA imports OpenOffice
Impress and Microsoft PowerPoint presentations and makes it
easy to add molecular animations.
|YASARA calculates Van der
Waals, molecular and solvent accessible volumes
|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.
|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.
|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 to
calculate solvation energies.
|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
to subdivide surfaces, the new operators 'with distance from
surface' and 'with contribution to surface' enable
||A summary of the science
behind YASARA is available in
movie format. (PhD thesis defence, 27th of September,
|Structural alignments are
handled by SHEBA via a Python plugin (Linux). New facilities
for building small molecules have been
|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
3D controller is now supported in Linux.
|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.
|YASARA calculates VdW,
molecular and solvent accessible surface areas.
Bert de Groot's CONCOORD program allows to quickly
analyze protein flexibility.
|YASARA's macro language
'Yanaconda' gets an extreme makeover, with lots of new
functions, better list handling and huge speedups.
|Adding chemical 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
the well 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 own
||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 Approach).
||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 ranked
first 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
||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 Twinset.
||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 texture
||New algorithm to display molecules in space-filling mode
with OpenGL and PVL, 35× faster than the usual approach.
||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 ready
and runs YASARA in parallel. See Bioinformatics
(2002) 18 , 315-318
||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 interface is
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
a parallel job scheduler.
||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
||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
||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
simulation on screen of a Pentium 133 (32 MB RAM): 1ACP, 768
atoms, space filling, quad-buffered stereo, 12 frames per
||The molecule rendering engine triples its speed thanks to
the 1st generation YAMAC (YASARA Molecule Accelerator, a
directly 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.