Dear All
I am planning to purify monoclonal antibody. In this concern
I found Pseudospecific ligands such as histidine, tryptophan,phenylalanine
etc. can be used to purify a wide range of bio-molecules and especially
immunoglobulin. I wish to know the structural mode of binding of Histidine
(as affinity ligand) with Immunoglobulin.
Sanjit Kumar
On Tue, May 13, 2014 at 5:03 AM, Paul Adams <[email protected]> wrote:
> The Phenix developers are pleased to announce that version 1.9 of Phenix
> is now available. Binary installers for Linux, Mac OSX, and Windows
> platforms are available at the download site:
>
> http://phenix-online.org/download/
>
> Highlights from this version:
>
> Significant changes to the content and presentation of documentation,
> major improvements to HySS and AutoSol for SAD phasing in cases of weak
> signal, new Phenix/Rosetta refinement program for difficult low resolution
> refinements, new real space refinement program for refinement against a
> density map (e.g. cryo-EM), feature enhanced maps (FEM) enhance weak
> features and reduce noise and bias, new composite omit map program, unified
> MolProbity validation program (consistent with the MolProbity web server),
> proximity restraints for group displacement parameter refinement in phenix
> refine, and option for automated chemical linking in phenix.refine.
>
> Graphical interface:
> ====================
> - Rearranged main interface to accompany documentation changes
> - New Phenix releases may be downloaded directly from the GUI (requires
> previously registered academic email address or permanent user
> credentials)
> - Added command to remove large data files (.geo, .kin, .ccp4, etc.) from
> a project directory to
> conserve disk space
> - Changes to support Mac OS 10.9 ("Mavericks")
>
> General:
> ========
> - Re-organized and updated documentation
> - Binary installers for Ubuntu (10.04 or later) available
> - Python built as shared library in Linux builds (facilitates Rosetta
> hybrid)
> - new commands: phenix.composite_omit_map, phenix.rosetta_refine,
> phenix.molprobity, phenix.sceds, phenix.fem, phenix.real_space_refine,
> and many smaller utilities
>
> Refinement:
> ===========
> - phenix.refine:
> - similarity restraints for group isotropic B-factor refinement
> - set by group_b_iso.use_restraints (default=True)
> - data/restraints targets weight is determined automatically; can be
> adjusted by setting group_b_iso.restraints_weight (larger value makes
> restraints stronger)
> - various rotamer handling bug fixes
> - Automatic linking generation in phenix.refine and other programs that
> require restraints can be requested using the parameters link_all=True
> - handles any appropriate ligand-protein or ligand-nucleic acid
> covalent
> bonds, including sugars, amino acid modifications, and other
> prosthetic
> groups
> - behavior can be adjusted by setting maximum bond distances parameters
> - added "bfactor" and "occupancy" keywords to atom selection syntax (also
> applies to phenix.pdbtools)
> - Integration with DivCon suite (http://www.quantumbioinc.com) for QM
> refinement of ligands (requires separate license and installation)
>
> - phenix.rosetta_refine (new command):
> - Hybrid Rosetta/Phenix refinement of protein X-ray crystal structures
> for difficult cases at low resolution
> - reference: DiMaio et al. (2013) Nature Methods
>
> - phenix.ensemble_refinement:
> - enabled use of experimental phases (MLHL target)
>
> - phenix.real_space_refine (new command):
> - tool to refine a model against a map (especially EM maps)
>
> - phenix.morph_model:
> - fixed serious bug present in versions 1449-1626 that resulted in
> incorrect
> offset being applied
>
> Experimental Phasing and Model Building:
> ========================================
> - HySS (phenix.hyss):
> - Substructure search much more fully automated:
> - Search first with Patterson seeds and direct method
> - If no clear solution, try more seeds, Phaser completion, and varying
> resolution
> - Full parallelization makes the search rapid
>
> - AutoSol:
> - Now much more powerful for weak SAD data:
> - Incorporates new automated Hyss search
> - Classic solvent flipping density modification after Resolve density
> modification
> - Tests several values of smoothing radius for solvent boundary
> identifcation for weak data
> - Iterates heavy-atom substructure search with Phaser completion
> including
> density after density modification and using model after
> model-building
> - Require solutions scored by correlation to be substantially better
> than
> altermatives before eliminating alternatives
> - Building with helices_strands_only set as default for data at lower
> than
> 3 Angstroms
>
> - AutoSol, AutoBuild, and LigandFit:
> - You can now specify the value of the test set flag for the free data
> with
> test_flag_value=xxxx
>
> Molecular Replacement:
> ======================
> - phenix.sceds (new command, formerly phaser.splitter):
> - implements normal mode-based domain finding method
> - reference: McCoy et al. (2013) Acta Cryst D69
>
> - phenix.find_alt_orig_sym_mate:
> - offset the produced MLAD value with log(0.9) to avoid
> negative values if identical structures were to be compared.
> Consequently older versions therefore yield MLAD values which are
> 0.10536 smaller than the current version.
>
> New commands:
> =============
> - phenix.rosetta_refine (new command):
> - Hybrid Rosetta/Phenix refinement of protein X-ray crystal structures
> for difficult cases at low resolution
> - reference: DiMaio et al. (2013) Nature Methods
>
> - phenix.molprobity (new command):
> - Unified validation tool for command-line users; similar to existing
> comprehensive validation in the Phenix GUI
> - optional output of script for viewing results in Coot, or kinemage file
>
> - phenix.composite_omit_map (new command):
> - Default method uses very fast iterative de-biasing procedure
> - Can also generate either a simple or composite omit map with refinement
> and optional simulated annealing
> - Will generate multiple map types at once
> - parallelizable on multi-core systems or managed clusters
>
> - phenix.sceds (new command, formerly phaser.splitter):
> - implements normal mode-based domain finding method
> - reference: McCoy et al. (2013) Acta Cryst D69
>
> - phenix.real_space_refine (new command):
> - tool to refine a model against a map (especially EM maps)
>
> - phenix.fem (new command):
> - Compute "feature-enhanced" map ("FEM") - this protocol modifies a
> 2mFo-DFc
> sigmaA-weighted map such that the resulting map has strengthened weak
> signal, if present, and a reduced amount of noise and model bias.
> - combines randomization and averaging, treatment of missing
> reflections,
> residual composite omit map, and histogram equalization
> - resulting maps are more interpretable and have less bias compared to
> the
> starting 2mFo-DFc map
> - very fast procedure, no refinement required
>
> - phenix.map_to_structure_factors (new command):
> - convert map into structure factors (also intended for EM)
>
> - phenix.angle (new command):
> - compute angle between two axes or two atom selections
>
> - phenix.model_model_distances (new command):
> - Given two PDB files compute distances per atom, residue, chain, model
> and
> overall. It is assumed (and asserted in the code!) that the amount and
> order of atoms in both files are identical.
>
> - phenix.fab_elbow_angle (new command):
> - Calculating Fragment Antigen-Binding (Fab) elbow angle
>
> - phenix.f000 (new command):
> - Given PDB file estimate F(0,0,0); includes atomic model and
> bulk-solvent
>
> Ligands:
> ========
> - phenix.ligand_identification:
> - Now you can use ligand cif files (in addition to .pdb files) to build
> your
> own custom ligand library. Just specify "Ligand directory" (GUI) or
> use
> keyword "ligand_dir" (command line) to tell the program to use .pdb or
> .cif
> files in your own ligand directory.
> - Bug fix to properly handle mtz labels when using difference maps.
>
> For a full list of changes see:
>
> http://www.phenix-online.org/documentation/CHANGES
>
> Please note that this publication should be used to cite use of Phenix:
>
> PHENIX: a comprehensive Python-based system for macromolecular structure
> solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis,
> N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve,
> A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J.
> S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221
> (2010).
>
> Full documentation is available here:
>
> http://www.phenix-online.org/documentation/
>
> There is a Phenix bulletin board:
>
> http://www.phenix-online.org/mailman/listinfo/phenixbb/
>
> Please consult the installer README file or online documentation for
> installation instructions.
>
> Direct questions and problem reports to the bulletin board or:
>
> [email protected] and [email protected]
>
> Commercial users interested in obtaining access to Phenix should visit the
> Phenix website for information about the Phenix Industrial Consortium.
>
> The development of Phenix is principally funded by the National Institute
> of
> General Medical Sciences (NIH) under grant P01-GM063210. We also
> acknowledge
> the generous support of the members of the Phenix Industrial Consortium.
>
> --
> Paul Adams
> Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley
> Lab
> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley
> Lab
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
> Vice President for Technology, the Joint BioEnergy Institute
> Laboratory Research Manager, ENIGMA Science Focus Area
>
> Building 64, Room 248
> Building 80, Room 247
> Building 978, Room 4126
> Tel: 1-510-486-4225, Fax: 1-510-486-5909
> http://cci.lbl.gov/paul
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 64R0121
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Louise Benvenue [ [email protected] ][
> 1-510-495-2506 ]
> --
>
