Last update 01 Nov 2024

Structural Genomix, Inc.

Private Company|

California, United States

Private Company|

California, United States

Last update 01 Nov 2024

Overview

Pipeline

Deal

Translational Medicine

Overview

Clinical Trials associated with Structural Genomix, Inc.

EUCTR2005-001721-29-IT / Not yet recruitingNot Applicable

An Open-Label, Single-Arm, Multi-Center, Phase 2 Study of Troxatyl troxacitabine Administered by Continuous Infusion in Patients with Acute Myeloid Leukemia AML in Second Salvage

Start Date20 Sep 2005

Sponsor / Collaborator

Structural Genomix, Inc.

100 Clinical Results associated with Structural Genomix, Inc.

0 Patents (Medical) associated with Structural Genomix, Inc.

Literatures (Medical) associated with Structural Genomix, Inc.

01 Sep 2005·Proteins: Structure, Function, and BioinformaticsQ3 · BIOLOGY

Structural analysis of a set of proteins resulting from a bacterial genomics project

Q3 · BIOLOGY

Article

Author: Winhoven, J. ; Feil, I. ; Molinari, J. ; Harris, T. J. R. ; Emtage, S. ; Noland, B. W. ; He, D. ; Maletic, M. ; Marsh, C. D. ; Kissinger, C. ; Pagarigan, B. ; Muller-Dieckmann, H. J. ; Miller, I. ; Wright, T. A. ; Adams, J. M. ; Schwinn, K. D. ; Hoda, K. ; Sanderson, W. E. ; Huber, A. ; Gajiwala, K. S. ; Sauder, J. M. ; Romero, R. ; Laubert, B. ; Christopher, J. A. ; Peat, T. S. ; Xu, J. ; Rutter, M. E. ; Loomis, K. ; Buchanan, M. D. ; Park, F. ; Wu, L. ; Newman, J. M. ; Bergseid, M. G. ; Tresser, J. ; Buchanan, S. G. ; Radojicic, S. ; Louie, G. ; Furlong, E. B. ; Badger, J. ; Hendle, J. ; Ramos, A. ; Eroshkina, A. ; Gao, X. ; Lorimer, D. ; Antonysamy, S. ; Batiyenko, Y. ; Post, K. W. ; Lewis, H. A. ; Bain, K. ; Lin, J. ; Kearins, P.

AbstractThe targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se‐Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X‐ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence‐structure relationships between the SGX and PDB structures were investigated using PDB‐BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB. Proteins 2005. © 2005 Wiley‐Liss, Inc.

01 May 2003·Acta Crystallographica Section D Biological Crystallography

An evaluation of automated model-building procedures for protein crystallography

Article

Author: Badger, John

The computer programs ARP/wARP, MAID and RESOLVE are designed to build protein structures into experimentally phased electron-density maps without any user intervention, requiring only diffraction data and sequence information. However, the MAID and RESOLVE systems, which seek to extend the range of automated model-building to approximately 3 A resolution, have yet to receive significant testing outside the small numbers of data sets used in their development. Since these two systems employ a large number of scoring functions and decision-making heuristics, additional tests are required to establish their usefulness to the crystallographic community. To independently evaluate these programs, their performance was tested using a database containing 41 experimentally phased maps between 1.3 and 2.9 A resolution from a diverse set of protein structures. At resolutions higher than 2.3 A the most successful program was ARP/wARP 6.0, which accurately built an average of 90% of the main chain. This system builds somewhat larger fractions of the model than the previous version ARP/wARP 5.1, which accurately built an average of 87% of the main chain. Although not specifically designed for model building into high-resolution maps, MAID and RESOLVE were also quite successful in this resolution regime, typically building approximately 80% of the main chain. At 2.3-2.7 A resolution the MAID and RESOLVE programs automatically built approximately 75% of the main-chain atoms in the protein structures used in these tests, which would significantly accelerate the model-building process. Data sets at lower resolution proved more problematic for these programs, although many of the secondary-structure elements were correctly identified and fitted.

01 Jan 2003·Methods of biochemical analysis

Structural genomics.

Review

Author: Burley, Stephen K ; Bonanno, Jeffrey B

100 Deals associated with Structural Genomix, Inc.

100 Translational Medicine associated with Structural Genomix, Inc.

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