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18-12-2014

Release of ARP/wARP 7.5

As of today the most recent ARP/wARP version (7.5) can be downloaded from http://www.arp-warp.org. This release is bundled with the ccp4 6.5 release.

Major changes in Version 7.5
  • Increased performance of protein model building through:
  • improved polypeptide recognition,
  • NCS-restraints,
  • atom update,
  • SAD-refinement option,
  • estimation of solvent content
  • and model accuracy

  • Improved stability of beta-strand, DNA/RNA and solvent building
  • "Fit Ligand" incorporates 84 most common ligands now and
  • uses cif files defining bond, torsion and plane restraints
  • Incremental improvements in auto-depth view and menus of ArpNavigator

15-09-2014

LASEROMIX: Established new international collaborational R&D project

We established the new R&D project Laseromix bringing together experts from EMBL, University Osnabrück and Moscow - including Moscow State University and Kurchatov center - to develop methods to exploit the remarkable potential for measuring 3D structures and dynamics of single bioparticles using Free Electron Lasers. Laseromix will standardise protocols for sample preparation, invent novel sample delivery methods consuming very low amounts of sample and most prominently will develop the first comprehensive software package to process the XFEL data and enable their biological interpretation.

18-07-2014

EMBL Labday

Taking part in the EMBL Labday 2014 and presenting "Construction and validation of macromolecular models"

29-06-2014

New paper published by C. Carolan and V. S. Lamzin

Automated identification of crystallographic ligands using sparse-density representations.
Carolan CG, Lamzin VS
A novel procedure for the automatic identification of ligands in macromolecular crystallographic electron-density maps is introduced. It is based on the sparse parameterization of density clusters and the matching of the pseudo-atomic grids thus created to conformationally variant ligands using mathematical descriptors of molecular shape, size and topology. In large-scale tests on experimental data derived from the Protein Data Bank, the procedure could quickly identify the deposited ligand within the top-ranked compounds from a database of candidates. This indicates the suitability of the method for the identification of binding entities in fragment-based drug screening and in model completion in macromolecular structure determination.
Acta Crystallogr D Biol Crystallogr. 2014 Jul;70(Pt 7):1844-53. doi: 10.1107/S1399004714008578. Epub 2014 Jun 29.   PUBMED

03-05-2014

New paper published by O. A. Petrova, E. M. Smekalova, M.E. Zvereva, V. Lamzin, O. A. Dontsova.

Identification of additional telomerase component of the yeast H. polymorpha is a step towards understanding the complex at the atomic level.
Petrova OA, Smekalova EM, Zvereva ME, Lamzin V, Dontsova OA
no abstract available
Dokl Biochem Biophys. 2014 Mar;455(1):59-64. doi: 10.1134/S1607672914020057. Epub 2014 May 3.   PUBMED

15-02-2014

New paper published by N. Ponomarenko, S. D. Chatziefthimiou SD, [...], V. Lamzin, [...], A. Gabibov.

Role of kappa-->lambda light-chain constant-domain switch in the structure and functionality of A17 reactibody.
Ponomarenko N, Chatziefthimiou SD, Kurkova I, Mokrushina Y, Mokrushina Y, Stepanova A, Smirnov I, Avakyan M, Bobik T, Mamedov A, Mitkevich V, Belogurov A Jr, Fedorova OS, Dubina M, Golovin A, Lamzin V, Friboulet A, Makarov AA, Wilmanns M, Gabibov A
The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophosphate-metabolizing reactibody A17 has been re-engineered by replacing its constant kappa light chain by the lambda chain (A17lambda), and the X-ray structure of A17lambda has been determined at 1.95 A resolution. It was found that compared with A17kappa the active centre of A17lambda is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the VL and VH domains. These VL/VH domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126 degrees compared with 138 degrees in A17kappa. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17kappa and A17lambda variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions.
Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):708-19. doi: 10.1107/S1399004713032446. Epub 2014 Feb 15.   PUBMED

01-02-2014

New group member!

Daria Beshnova has joined our group as a new EIPOD-Postdoc. Daria is working on software development for ligand identification within the ARP/wARP software project.

09-10-2013

Release of ARP/wARP 7.4

As of today the most recent ARP/wARP version (7.4) can be downloaded from http://www.arp-warp.org. This release will also be bundled with the upcoming ccp4 6.4.

Major changes in Version 7.4
  • The use of non-crystallographic symmetry for protein chain tracing has been further improved. On average, the built protein models are now 5% more complete and the built fragments are 50% longer. The NCS order is automatically adjusted according to the expected solvent content.
  • An alpha version of a new algorithm called Faked Data has been introduced, which additionally improves protein model building at a resolution around 2.5-3.0 Å.
  • Rfree set (0 or 1) is recognised automatically.
  • New checks are introduced to interpret the input amino-acid sequence. Additionally, on Mac OSX the sequence given in rich-text format can now be interpreted.
  • The accuracy of the estimation of the model correctness has been improved from an error of 3.0 to 2.5%.
  • The algorithm for fitting partial ligands into an electron density (cocktail screening) has been replaced with a new method that applies a number of sophisticated features and considers multiple conformations of the ligand fragments.
  • ARP/wARP identifies and fits more ligands into a specified electron density, with the protocols being faster and more sophisticated. 84 of the most common ligands in the PDB, including typically-encountered coenzymes, buffer constituents and cryo-protectant compounds are screened in all conformations against a user-defined density cluster and the best-fitting compound modelled. The protocol is conveniently and intuitively accessible from the ARP Navigator interface.
  • ARP/wARP now utilises cif files that define bond, torsion and plane restraints for ligand fitting.
  • The three-letter PDB code for a ligand can be provided as an input to ligand building via CCP4i instead of a PDB structure.
  • The ARP/wARP CCP4i interface has been extended to accommodate accumulated developments.
  • The ARP Navigator has been made more robust, the default appearance and object rastering have been made nicer. The software now works seamlessly on Mac OSX 10.8.
  • To ensure a smoother user experience, the "Quick Action"-Menu in ARP Navigator has been considerably improved. Additionally, a new button 'Submit to ViCi' has been added (ViCi is a new web-server for in-silico ligand-based drug design).
  • Supported computer platforms are Mac Intel (10.5 to 10.8) and Linux (both 32 and 64-bit versions).
  • The ARP/wARP installer has been considerably modified and became more robust. There is no need anymore to source ARP/wARP setup files in .cshrc/bash_profile. By sourcing the CCP4 setup ARP/wARP the settings to source ARP/wARP will be installed automatically for the following login shells: csh, tcsh, sh, bash, zsh.
  • CCP4 6.4.0 and Refmac 5.7.0032 (or higher) are the recommended versions to use with ARP/wARP 7.4.

07-08-2013

Ciaran got EMBL Outstanding Postdoc Award

From the EMBL&cetera newsletter:
Five finalists presented research in areas including evolutionary biology, cancer genomics and structural biology. Selected by participants, Ciaran Carolan (Lamzin group) won, with his talk exploring the discovery and testing of novel b-Lactam inhibitors. "It's an honour to receive this award, which also recognises the important contributions to the project by EMBL colleagues and our collaborators in Moscow," said Ciaran.

20-07-2013

Tim got the Warren DeLano Structural Bioinformatics and Computational Biophysics award

From the EMBL&cetera newsletter:
Breaking down complex science to something as simple as cats and dogs is no easy task. EMBL Hamburg postdoc Tim Wiegels wowed judges at the 3DSIG satellite meeting at this year's ISMB conference by doing just that, scooping the Warren DeLano Structural Bioinformatics and Computational Biophysics award for his presentation exploring bioinformatics methods to improve structural models in X-ray crystallography. "Using something so simple to explain pattern recognition - essentially the transformation of signals to meaning using available knowledge - grabs peoples' attention and can help them to understand better: for example, you know that pugs look different than French bulldogs and if you see a shadow with pointy ears, it's easy to deduce which dog fits," says Tim. "I am delighted the judges have recognised something that I have enjoyed doing for a long time now."

01-04-2013

Made it to the title!

Latest ArpNavigator paper became title of Acta D (Volume 69, Part 4 (April 2013))!



29-03-2013

ARP/wARP around the world

The ARP/wARP team will be present at several upcomming workshops and schools again:

Ciaran Carolan will be at MMX School 2013 "From data processing to structure refinement and beyond" in Montevideo, Uruguay (April 9th-17th, 2013)

Tim Wiegels will be at the APS Data collection workshop and CCP4 school: From data collection to structure refinement and beyond; June 18 - June 26 2013 in Chicago, USA

14-03-2013

New paper published by G. G. Langer, S. Hazledine, T. Wiegels, C. Carolan and V. S. Lamzin

Visual automated macromolecular model building.
Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS
Automated model-building software aims at the objective interpretation of crystallographic diffraction data by means of the construction or completion of macromolecular models. Automated methods have rapidly gained in popularity as they are easy to use and generate reproducible and consistent results. However, the process of model building has become increasingly hidden and the user is often left to decide on how to proceed further with little feedback on what has preceded the output of the built model. Here, ArpNavigator, a molecular viewer tightly integrated into the ARP/wARP automated model-building package, is presented that directly controls model building and displays the evolving output in real time in order to make the procedure transparent to the user.
Acta Crystallogr D Biol Crystallogr. 2013 Apr;69(Pt 4):635-41. doi: 10.1107/S0907444913000565. Epub 2013 Mar 14.   PUBMED

01-12-2012

New group member!

Joana Pereira has joined our group as a new predoc. Joana is working on software development within the ARP/wARP software project.

01-12-2012

ARP/wARP around the world

Meet us at the CCP4 Study Weekend (3 - 5 January 2013) in Nottingham!

22-08-2012

ViCi for ligand-based drug screening now online

EMBL Hamburg's new software for ligand-based drug screening, ViCi, is now live and accessible to the general community at the following webpage:

http://www.embl-hamburg.de/vici/index

ViCi is an innovative software for ligand-based drug design available free of charge to academic researchers via this webserver. ViCi uses a combination of mathematical descriptors of molecular size, shape and topology to describe small molecule structures. Following input of a template molecule, typically that of a known ligand in its bound conformation in a particular protein, the software will rapidly screen a database (currently 8 million compounds) and extract those predicted to have similar shape and electrostatic compositions and therefore to be possible ligands for the same protein. Results are typically obtained in a matter of hours and are returned to the user ranked by probability of binding.

13-08-2012

New group member!

Claudia Hackenberg has joined our group as a new postdoc. Claudia will strengthen our wet lab work, in particular with respect to the development of new techniques for XFEL related sample handling and preparation.

06-08-2012

ARP/wARP around the world

Meet us at the ECM in Bergen (6-11.08.2012): Presentations by Tim and Ciaran on recent novel developments within ARP/wARP; Meet us in person at the CCP4 info booth!
  • 08.08.: 11:20; Ciaran Carolan - Automated Identification of Ligands in Macromolecular Electron Density Maps
  • 9.8.: 15:30; Tim Wiegels - Software Fayre
  • 10.08.: 11:00; Tim Wiegels - Structural bioinformatics incorporated into ARP/wARP model building
  • Poster MS7-P1 Discovery of Novel Inhibitors of Bacterial beta-Lactamases using ARP/wARP-based Drug Design
  • Poster MS49-P3 The ARP/wARP model building suite and the Arpnavigator user interface.

01-08-2012

New group member!

Ioan Vancea has joined our group as a software developer. Ioan will be responsible for maintenance of ARP/wARP and the implementation of novel developments into ARP/wARP. Welcome Ioan!

24-07-2012

Impact factor of 12.6 for Acta Crystallographica Section D Biological Crystallography

Thomson Reuters have released their 2011 Journal Citation Reports, where Acta Crystallographica Section D Biological Crystallography leads the crystallography rankings with its highest ever impact factor of 12.6. This is a marked success of structural biology, and is a reward of many EMBL-Hamburg employees who publish in this journal or cite the papers published therein. Over the years the Lamzin group has published more than 30 papers in Acta Cryst D.

16-07-2012

ARP/wARP 7.3 corelease with CCP4 6.3.0

Release 6.3.0 marks a milestone in collaboration between CCP4 and ARP/wARP teams by releasing ARP/wARP Model Building software v7.3 jointly with CCP4 Software Suite. In order to get ARP/wARP Software, academic users need only to select the appropriate package from download pages or with the new CCP4 Package Manager, and type in their name and e-mail address where required. Commerical users will be required also to provide their reference number, obtainable separately from EMBL-EM.

The CCP4 software suite is the world's most comprehensive collection of crystallographic software and for the first time advances of ARP/wARP, developed at the EMBL Hamburg, was fully packaged into a user-friendly bundle with CCP4. Although ARP/wARP has always been compatible with the CCP4 software, data model and style, the need to download and install two separate packages has been a hurdle for novice users. Now, both packages are available together with a single mouse click. This joint release is an acknowledgment of the hard work invested by the research team at EMBL Hamburg, and recognition of ARP/wARP as one of the leading software solutions for building of macromolecular structures.

ARP/wARP 7.3 includes the following major updates and changes:

  • The protocols for the use of NCS in protein chain tracing have been improved and expanded to a wider range of resolutions.
  • Common ligands can now be automatically identified and fit into a specified electron density.
  • The algorithm for modelling partial ligands (cocktail screening) has been replaced with a new one that applies a number of sophisticated numerical features
  • The ARP/wARP graphics front-end, ArpNavigator, automatically assigns secondary structure and has an improved visual presentation of a static model or real time protein or ligand building.
  • Supported computer platforms are Mac powerpc, Mac Intel and Linux (including 32 and 64-bit versions).
  • The ARP/wARP installer has been considerably updated on all platforms.
  • Joint software release and authentication with the CCP4 is now possible.
  • CCP4 6.3.0 and Refmac 5.7.0029 are the recommended versions to use with ARP/wARP 7.3.

01-06-2012

The dream of an integrated Biology Infrastructure Life Science Facility at the European XFEL project in Hamburg is one step closer to realisation.

EMBL etcetera on XBI: Victor Larnzin, deputy head of EMBL Hamburg, is coordinating a project to construct, commission, and operate a Biology infrastructure Life Science Center (XBI) at the European XFEL project. [...] The nature of modern structural biology experiments and the fragility and short life span of many samples, mean the ability to prepare, analyse, and interpret experiments in immediate proximity to the XFEL instruments is essential. The project will develop a dedicated infrastructure to support this.

The XBI project was recommended for implementation at the XFEL Council meeting in June and follows the signing of a Memorandum of Understanding by EMBL and XFEL in September 2011 as a basis for future collaborations.[...] "The underlying international and inter-institutional activities will make XBI the world's premier centre in XFEL biological imaging" Victor adds.
Read more

01-05-2012

New group member!

Thomas Margraf has joined our group as an EIPOD-Postdoc. Thomas is affiliated as well to our group as to John Briggs group in Heidelberg. Welcome Thomas!

23-03-2012

New paper out by Langer GG, Evrard GX, Carolan CG, Lamzin VS.

Fragmentation-tree density representation for crystallographic modelling of bound ligands.
Langer GG, Evrard GX, Carolan CG, Lamzin VS
The identification and modelling of ligands into macromolecular models is important for understanding molecule's function and for designing inhibitors to modulate its activities. We describe new algorithms for the automated building of ligands into electron density maps in crystal structure determination. Location of the ligand-binding site is achieved by matching numerical shape features describing the ligand to those of density clusters using a "fragmentation-tree" density representation. The ligand molecule is built using two distinct algorithms exploiting free atoms with inter-atomic connectivity and Metropolis-based optimisation of the conformational state of the ligand, producing an ensemble of structures from which the final model is derived. The method was validated on several thousand entries from the Protein Data Bank. In the majority of cases, the ligand-binding site could be correctly located and the ligand model built with a coordinate accuracy of better than 1 A. We anticipate that the method will be of routine use to anyone modelling ligands, lead compounds or even compound fragments as part of protein functional analyses or drug design efforts.
J Mol Biol. 2012 Jun 8;419(3-4):211-22. doi: 10.1016/j.jmb.2012.03.012. Epub 2012 Mar 23.   PUBMED

16-03-2012

New paper out by Wiegels T, Lamzin VS.

Use of noncrystallographic symmetry for automated model building at medium to low resolution.
Wiegels T, Lamzin VS
A novel method is presented for the automatic detection of noncrystallographic symmetry (NCS) in macromolecular crystal structure determination which does not require the derivation of molecular masks or the segmentation of density. It was found that throughout structure determination the NCS-related parts may be differently pronounced in the electron density. This often results in the modelling of molecular fragments of variable length and accuracy, especially during automated model-building procedures. These fragments were used to identify NCS relations in order to aid automated model building and refinement. In a number of test cases higher completeness and greater accuracy of the obtained structures were achieved, specifically at a crystallographic resolution of 2.3 A or poorer. In the best case, the method allowed the building of up to 15% more residues automatically and a tripling of the average length of the built fragments.
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):446-53. doi: 10.1107/S0907444911050712. Epub 2012 Mar 16.   PUBMED

01-03-2012

New paper out by Wrenger C, Müller IB, Silber AM, Jordanova R, Lamzin VS, Groves MR.

Aspartate aminotransferase: bridging carbohydrate and energy metabolism in Plasmodium falciparum.
Wrenger C, Muller IB, Silber AM, Jordanova R, Lamzin VS, Groves MR
In this mini-review we briefly examine and summarize evidence on the role of the plasmodial aspartate aminotransferase (AspAT) of the malarial parasite. Recent data have provided information on the products of the purine salvage pathway as well as the glycolytic and oxidative phosphorylation pathways, suggesting that the reaction catalyzed by AspAT is an essential step in all these biochemical processes. While the biological role of the oxidative phosphorylation cycle still remains to be demonstrated, the presence of a single protein that is functional in multiple pathways (i.e. amino acid/purine/pyrimidine biosynthesis and carbohydrate metabolism) provides a high potential for the development of novel strategies to combat the spread of multi-drug resistant malaria.
Curr Drug Metab. 2012 Mar;13(3):332-6.   PUBMED

02-02-2012

ARP/wARP around the world

Upcoming ARP/wARP tutorials at CCP4 School on advanced X-ray crystal structure analysis in Melbourne (Australia) in Feb 2012, at the Course for computational methods for macromolecular phasing and refinement in Zaragoza (Spain) in March 2012, and at the 5th annual CCP4 USA Crystallography School at the Advanced Photon Source (APS) synchrotron near Chicago in June 2012

24-01-2012

Questionnaire on Biology infrastructure at the XFEL

The European Molecular Biology Laboratory (EMBL) and the European X-ray Free Electron Laser (XFEL) at DESY, Hamburg, Germany, have a keen interest in the development of FEL-based applications in structural biology. Within this framework the EMBL, together with international collaborators from Russia, Sweden and Germany, propose to construct a biology infrastructure at the XFEL facility (expected completion in 2016) to enable biological experiments using the high brilliance, ultrashort pulse duration and high repetition rate coherent X-ray radiation.
The proposed biological sample infrastructure facility will provide:
- support to the international life-science community in generation and handling of challenging samples in immediate proximity to XFEL instruments.
- appropriate selection, quality control and evaluation of samples, including correlative imaging, immediately prior to XFEL experiments.
- standardized technology for data interpretation, including computation and validation of structural models.
In order to ensure efficient operation of the facility and provide optimal services for the international biological community we seek your input to identify the requirements necessary to support these novel biological imaging experiments. We would appreciate your input in the web-based questionnaire available at http://www.embl-hamburg.de/xfel_cgi-bin/questionnaire The results of this survey will be used to identify the most pressing needs that should be taken into account during planning and construction of the infrastructure. We thank you in advance for your cooperation.

22-08-2011

ARP/wARP 7.2

We are happy to announce the release of ARP/wARP version 7.2. Please visit http://www.arp-warp.org for details, software download or remote submission of protein model building.

The major implementations and improvements are:

* The functionality of the graphics front-end, Arp Navigator, has been considerably extended.

* Auto-NCS detection coupled with enhanced protein chain tracing helps obtain more complete models, particularly at resolution lower than 2.5 Å.

* Automated ligand building can screen a cocktail of candidates and has an option to model bound ligands that are partially ordered.

* Supported computer platforms are Mac powerpc, Mac Intel and Linux (including 32 and 64-bit versions).

* The ARP/wARP installer has been updated on all platforms so that its use should be simpler for the users. Users of Mac OSX Intel can also download and install a native application packaged in a DMG file.

* There should be full compatibility of ARP/wARP 7.2 with with CCP4 6.1.13 and Refmac 5.5.0109.

04-08-2011

Meet us at the IUCr2011 in Madrid (22-30 August 2011)

We will be at the IUCr in Madrid. There will be four presentations by the Lamzin Group:

Philipp Heuser Pattern recognition for modelling in very low resolution density maps (MS02 Tue 23/08/ 10:15-12:50)

Tim Wiegels Release 7.2 of ARP/wARP Software Suite (Talk in MS58, Sa 27/08/ 10:15-12:50)
Towards more complete models in macromolecular crystal structure determination (Poster, abstract No. 909 in MS 58)

Tutorial @ Crystallographic Software Fayre ARP/wARP for building models of proteins and their binding partners (Fri 26/08/, 16:15-17:00)

12-07-2011

New paper out by Unge J, Mueller-Dieckmann C, Panjikar S, Tucker PA, Lamzin VS, Weiss MS.

On the routine use of soft X-rays in macromolecular crystallography. Part V. Molecular replacement and anomalous scattering.
Unge J, Mueller-Dieckmann C, Panjikar S, Tucker PA, Lamzin VS, Weiss MS
Currently, about two thirds of all new macromolecular structures are determined by molecular replacement. In general the method works reliably, but it reaches its limits when the search model differs too much from the target structure in terms of coordinate deviations or completeness. Since anomalously scattering substructures are better conserved than the overall structure, these substructures and the corresponding anomalous intensity differences can be utilized to enhance the performance of molecular-replacement approaches. It is demonstrated that the combined and concomitant use of structure-factor amplitudes and anomalous differences constitutes a promising approach to push the limits of molecular replacement and to make more structures amenable to structure solution by this technique.
Acta Crystallogr D Biol Crystallogr. 2011 Aug;67(Pt 8):729-38. doi: 10.1107/S0907444911024887. Epub 2011 Jul 12.   PUBMED

01-07-2011

New Internet Page for the Lamzin Group

We hope you do like our new webpage released today

01-05-2011

New group member!

Saul Hazeldine has joined our group as a Scientific Programmer, continuing the work of Gerrit Langer on the development of the Arp Navigator, and the maintenance of the ARP/wARP code and its release! Welcome Saul!

24-03-2011

New paper out by Schmidt A, Teeter M, Weckert E and Lamzin VS

Crystal structure of small protein crambin at 0.48 A resolution.
Schmidt A, Teeter M, Weckert E, Lamzin VS
With the development of highly brilliant and extremely intense synchrotron X-ray sources, extreme high-resolution limits for biological samples are now becoming attainable. Here, a study is presented that sets the record in crystallographic resolution for a biological macromolecule. The structure of the small protein crambin was determined to 0.48 A resolution on the PETRA II ring before its conversion to a dedicated synchrotron-radiation source. The results reveal a wealth of details in electron density and demonstrate the possibilities that are potentially offered by a high-energy source. The question now arises as to what the true limits are in terms of what can be seen at such high resolution. From what can be extrapolated from the results using crystals of crambin, this limit would be at approximately 0.40 A, which approaches that for smaller compounds.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Apr 1;67(Pt 4):424-8. doi: 10.1107/S1744309110052607. Epub 2011 Mar 24.   PUBMED

04-08-2010

New publication by J. Hattne and V.S. Lamzin

A moment invariant for evaluating the chirality of three-dimensional objects.
Hattne J, Lamzin VS
Chirality is an important feature of three-dimensional objects and a key concept in chemistry, biology and many other disciplines. However, it has been difficult to quantify, largely owing to computational complications. Here we present a general chirality measure, called the chiral invariant (CI), which is applicable to any three-dimensional object containing a large amount of data. The CI distinguishes the hand of the object and quantifies the degree of its handedness. It is invariant to the translation, rotation and scale of the object, and tolerant to a modest amount of noise in the experimental data. The invariant is expressed in terms of moments and can be computed in almost no time. Because of its universality and computational efficiency, the CI is suitable for a wide range of pattern-recognition problems. We demonstrate its applicability to molecular atomic models and their electron density maps. We show that the occurrence of the conformations of the macromolecular polypeptide backbone is related to the value of the CI of the constituting peptide fragments. We also illustrate how the CI can be used to assess the quality of a crystallographic electron density map.
J R Soc Interface. 2011 Jan 6;8(54):144-51. doi: 10.1098/rsif.2010.0297. Epub 2010 Aug 4.   PUBMED

10-07-2010

New publication by D.Watts, J. Müller-Dieckmann, G. Tsakanova, V.S. Lamzin and M.R. Groves

Quantitive evaluation of macromolecular crystallization experiments using 1,8-ANS fluorescence.
Watts D, Muller-Dieckmann J, Tsakanova G, Lamzin VS, Groves MR
Modern X-ray structure analysis and advances in high-throughput robotics have allowed a significant increase in the number of conditions screened for a given sample volume. An efficient evaluation of the increased amount of crystallization trials in order to identify successful experiments is now urgently required. A novel approach is presented for the visualization of crystallization experiments using fluorescence from trace amounts of a nonspecific dye. The fluorescence images obtained strongly contrast protein crystals against other phenomena, such as precipitation and phase separation. Novel software has been developed to quantitatively evaluate the crystallization outcome based on a biophysical metric correlated with voxel protein concentration. In >1500 trials, 85.6% of the successful crystallization experiments were correctly identified, yielding a 50% reduction in the number of 'missed hits' compared with current automated approaches. The use of the method in the crystallization of three previously uncharacterized proteins from the malarial parasite Plasmodium falciparum is further demonstrated.
Acta Crystallogr D Biol Crystallogr. 2010 Aug;66(Pt 8):901-8. doi: 10.1107/S0907444910020664. Epub 2010 Jul 10.   PUBMED

02-03-2010

New publication by A.Schmidt and V.S. Lamzin

Internal motion in protein crystal structures.
Schmidt A, Lamzin VS
The binding states of the substrates and the environment have significant influence on protein motion. We present the analysis of such motion derived from anisotropic atomic displacement parameters (ADPs) in a set of atomic resolution protein structures. Local structural motion caused by ligand binding as well as functional loops showing cooperative patterns of motion could be inferred. The results are in line with proposed protonation states, hydrogen bonding patterns and the location of distinctly flexible regions: we could locate the mobile active site loop in a virus integrase, distinguish the subdomains in RNAse A and hydroxynitrile lyase, and reconstruct the molecular architecture in a xylanase. We demonstrate that the ADP-based motion analysis provides information at high level of detail and that the structural changes needed for substrate attachment or release may be derived from single X-ray structures.
Protein Sci. 2010 May;19(5):944-53. doi: 10.1002/pro.371.   PUBMED

24-12-2009

ARP/wARP 7.1 released

We are happy to announce the release of ARP/wARP version 7.1.
Please visit http://www.arp-warp.org for details and software download.
The major implementations and improvements are:
  • A prototype of the molecular graphics ARP/wARP front-end, allowing the display of molecules and electron densities.
  • A prototype version of the new module for building poly-nucleotides (DNA or RNA).
  • Improved and faster protein chain tracing with higher performance at lower resolution.
  • The loop building as well as helix/strand building are now also inherent parts of protein model building, resulting in enhanced model completeness.
  • Refinement procedures during automated model building have been enhanced in the new versions of our preferred refinement engine, REFMAC, notably including the implementation of 'conditional restraints'.
  • Direct use of experimental single-wavelength anomalous diffraction data (SAD) during model building is now also possible.
  • Improved performance of automated ligand building.
  • Supported computer platforms are Mac powerpc, Mac Intel and Linux (including 32 and 64-bit versions and itanium).

Merry Xmas and Happy New Year!

© by VL-Group 2011