Nature Methods: doi: /nmeth Supplementary Figure 1. Overview of the density-guided rebuilding and refinement protocol.
|
|
|
- Malcolm Carpenter
- 5 years ago
- Views:
Transcription
1 Supplementary Figure 1 Overview of the density-guided rebuilding and refinement protocol. (a) Flowchart of the protocol. The protocol uses 250 cycles of local backbone rebuilding, followed by five cycles of alternating coordinate and B factor refinement. (b) An inset illustrating the new density-guided rebuilding step. A segment with poor fit to density is selected at random. Next, different backbone conformations consistent with the local sequence are first superimposed on the current model, then optimized into the map. Finally, the best fitting backbone conformation is selected, and backbone geometry near the segment is regularized.
2 Supplementary Figure 2 Model quality as a function of map resolution. For a given starting model of 20S, we compare refined model accuracy (the fraction of Cα atoms within 1 Å of the reference model on the y-axis) as a function of map resolution for Rosetta-refined models (solid) and MDFF-refined models (dashed). The comparison used (A) 1yar, (B) 1ryp and (C) 1m4y as representatives of easy, medium, and difficult refinement cases, respectively.
3 Supplementary Figure 3 Identification of model errors using the local density correlation. For each refined model of 20S, local correlation between each residue and the testing map is calculated. The fraction of residues deviate more than 1Å (black) or 2Å (green) from the reference model (y-axis) is plotted for each local correlation bin (x-axis) at (A) 3.3, (B) 4.1, (C) 4.4, and (D) 6.0Å resolutions.
4 Supplementary Figure 4 Cross-validation of Rosetta-refined models using FSC. The FSC (y-axis) is compared to the accuracy of refined models (x-axis). Refinement is carried out with reconstructed maps of (A) 20S proteasome at (magenta) 3.3Å, (cyan) 4.1 Å, (red) 4.4 Å, (blue) 5.0 Å and (green) 6.0 Å, and with maps of (B) prgh needle complex at (red) 4.6 Å, (blue) 5.4 Å and (green) 7.1 Å.
5 Supplementary Figure 5 An overview of map features necessary for accurate structure determination. (a) The 20S proteasome dataset at 4.1 Å nicely illustrates the necessary features for structure determination to atomic accuracy. The pitch of helices and individual strands are resolved, and while sidechains are not uniquely identifiable density for large sidechains is visible. (b) The same dataset at 6 Å resolution lacks these features: the pitch of helices in not identifiable, and sidechain density for large sidechains is not observed.
6 Supplementary Information Supplementary Table 1. A comparison to previously published methods. For a series of comparative models of 20S, our refinement was compared to two previously developed methods combining Rosetta refinement with experimental density data, comparing the fraction of Cα atoms within 1 Å using the same starting models. DiMaio as well as RosettaCM 2 augmented with fit-to-density-energy are both outperformed by the IterativeBuild method reported here. Results are reported for 20S maps at 3.3 and 4.4Å resolution. 20S proteosome (3.3Å) 20S proteosome (4.4Å) DiMaio 2009 Rosetta CM Iterative Build DiMaio 2009 Rosetta CM Iterative Build 1yar h4p iru unf nzj ryp q5q g0u hnz x3b g3k m4y Average
7 Supplementary References 1 DiMaio, F., Tyka, M. D., Baker, M. L., Chiu, W. & Baker, D. Refinement of protein structures into low-resolution density maps using rosetta. Journal of molecular biology 392, (2009). 2 Song, Y. et al. High-Resolution Comparative Modeling with RosettaCM. Structure 21, (2013). 3
Supplementary Figures. Measuring Similarity Between Dynamic Ensembles of Biomolecules
Supplementary Figures Measuring Similarity Between Dynamic Ensembles of Biomolecules Shan Yang, Loïc Salmon 2, and Hashim M. Al-Hashimi 3*. Department of Chemistry, University of Michigan, Ann Arbor, MI,
Protein Dynamics. The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron.
Protein Dynamics The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron. Below is myoglobin hydrated with 350 water molecules. Only a small
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X ray Crystal Structures
pubs.acs.org/jacs Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X ray Crystal Structures Binchen Mao, Roberto Tejero,, David Baker, and Gaetano T. Montelione*,
Atomic structure and handedness of the building block of a biological assembly
Supporting Information: Atomic structure and handedness of the building block of a biological assembly Antoine Loquet, Birgit Habenstein, Veniamin Chevelkov, Suresh Kumar Vasa, Karin Giller, Stefan Becker,
Supplementary information for:
SUPPLEMETARY IFRMATI Supplementary information for: Structure of a β 1 -adrenergic G protein-coupled receptor Tony Warne, Maria J. Serrano-Vega, Jillian G. Baker#, Rouslan Moukhametzianov, Patricia C.
Molecular Modeling lecture 2
Molecular Modeling 2018 -- lecture 2 Topics 1. Secondary structure 3. Sequence similarity and homology 2. Secondary structure prediction 4. Where do protein structures come from? X-ray crystallography
Electron Density at various resolutions, and fitting a model as accurately as possible.
Section 9, Electron Density Maps 900 Electron Density at various resolutions, and fitting a model as accurately as possible. ρ xyz = (Vol) -1 h k l m hkl F hkl e iφ hkl e-i2π( hx + ky + lz ) Amplitude
Protein Structure Refinement Using 13 C α Chemical. Shift Tensors. Benjamin J. Wylie, Charles D. Schwieters, Eric Oldfield and Chad M.
Protein Structure Refinement Using 13 C α Chemical Shift Tensors Benjamin J. Wylie, Charles D. Schwieters, Eric Oldfield and Chad M. Rienstra * Department of Chemistry, University of Illinois at Urbana-Champaign,
Supplementary Figure 1 Crystal contacts in COP apo structure (PDB code 3S0R)
Supplementary Figure 1 Crystal contacts in COP apo structure (PDB code 3S0R) Shown in cyan and green are two adjacent tetramers from the crystallographic lattice of COP, forming the only unique inter-tetramer
Template Free Protein Structure Modeling Jianlin Cheng, PhD
Template Free Protein Structure Modeling Jianlin Cheng, PhD Associate Professor Computer Science Department Informatics Institute University of Missouri, Columbia 2013 Protein Energy Landscape & Free Sampling
SUPPLEMENTARY INFORMATION
Supplementary Results DNA binding property of the SRA domain was examined by an electrophoresis mobility shift assay (EMSA) using synthesized 12-bp oligonucleotide duplexes containing unmodified, hemi-methylated,
Supporting Information
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2016 Supporting Information Lipid molecules can induce an opening of membrane-facing
Protein Structure Determination from Pseudocontact Shifts Using ROSETTA
Supporting Information Protein Structure Determination from Pseudocontact Shifts Using ROSETTA Christophe Schmitz, Robert Vernon, Gottfried Otting, David Baker and Thomas Huber Table S0. Biological Magnetic
Cryo-EM data collection, refinement and validation statistics
1 Table S1 Cryo-EM data collection, refinement and validation statistics Data collection and processing CPSF-160 WDR33 (EMDB-7114) (PDB 6BM0) CPSF-160 WDR33 (EMDB-7113) (PDB 6BLY) CPSF-160 WDR33 CPSF-30
Part 7 Bonds and Structural Supports
Part 7 Bonds and Structural Supports http://cbm.msoe.edu/newwebsite/learntomodel Introduction In addition to covalent bonds between atoms in a molecule, Jmol has the ability to render Hydrogen Bonds and
Full wwpdb NMR Structure Validation Report i
Full wwpdb NMR Structure Validation Report i Feb 17, 2018 06:22 am GMT PDB ID : 141D Title : SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GENOME: RESTRAINED MOLECULAR DYNAMICS SIMU- LATION
EM-Fold: De Novo Atomic-Detail Protein Structure Determination from Medium-Resolution Density Maps
Article EM-Fold: De Novo Atomic-Detail Protein Structure Determination from Medium-Resolution Density Maps Steffen Lindert, 1 Nathan Alexander, 1 Nils Wötzel, 1 Mert Karakasx, 1 Phoebe L. Stewart, 2 and
Bonds and Structural Supports
Bonds and Structural Supports Part of the Jmol Training Guide from the MSOE Center for BioMolecular Modeling Interactive version available at http://cbm.msoe.edu/teachingresources/jmol/jmoltraining/struts.html
SUPPLEMENTARY INFORMATION
SUPPLMTARY IFORMATIO a doi:10.108/nature10402 b 100 nm 100 nm c SAXS Model d ulers assigned to reference- Back-projected free class averages class averages Refinement against single particles Reconstructed
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker Presented by Kate Stafford 4 May 05 Protein
SUPPLEMENTARY INFORMATION
doi:10.1038/nature11054 Supplementary Fig. 1 Sequence alignment of Na v Rh with NaChBac, Na v Ab, and eukaryotic Na v and Ca v homologs. Secondary structural elements of Na v Rh are indicated above the
Orientational degeneracy in the presence of one alignment tensor.
Orientational degeneracy in the presence of one alignment tensor. Rotation about the x, y and z axes can be performed in the aligned mode of the program to examine the four degenerate orientations of two
SUPPLEMENTARY INFORMATION
www.nature.com/nature 1 Figure S1 Sequence alignment. a Structure based alignment of the plgic of E. chrysanthemi (ELIC), the acetylcholine binding protein from the snail Lymnea stagnalis (AchBP, PDB code
Protein Structure Prediction
Protein Structure Prediction Michael Feig MMTSB/CTBP 2009 Summer Workshop From Sequence to Structure SEALGDTIVKNA Folding with All-Atom Models AAQAAAAQAAAAQAA All-atom MD in general not succesful for real
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11600 Contents Supplementary Discussion 1 Emergent rules.... 3 Supplementary Figure 1 Emergent rules.... 5 Supplementary Figure 2 Torsion energies of loops are
SUPPLEMENTARY MATERIAL FOR
SUPPLEMENTARY MATERIAL FOR THE LIPID-BINDING DOMAIN OF WILD TYPE AND MUTANT ALPHA- SYNUCLEIN: COMPACTNESS AND INTERCONVERSION BETWEEN THE BROKEN- AND EXTENDED-HELIX FORMS. Elka R. Georgieva 1, Trudy F.
Supplementary Information. Cryo-EM Studies of Drp1 Reveal Cardiolipin Interactions that Activate
Supplementary Information Cryo-EM Studies of Drp1 Reveal Cardiolipin Interactions that Activate the Helical Oligomer Christopher A. Francy 1, 2, 3, Ryan W. Clinton 1, 2, 3, Chris Fröhlich 4, 5, Colleen
Protein Structure Prediction
Page 1 Protein Structure Prediction Russ B. Altman BMI 214 CS 274 Protein Folding is different from structure prediction --Folding is concerned with the process of taking the 3D shape, usually based on
Magnetic Resonance Lectures for Chem 341 James Aramini, PhD. CABM 014A
Magnetic Resonance Lectures for Chem 341 James Aramini, PhD. CABM 014A jma@cabm.rutgers.edu " J.A. 12/11/13 Dec. 4 Dec. 9 Dec. 11" " Outline" " 1. Introduction / Spectroscopy Overview 2. NMR Spectroscopy
Three-dimensional structure of a viral genome-delivery portal vertex
Three-dimensional structure of a viral genome-delivery portal vertex Adam S. Olia 1, Peter E. Prevelige Jr. 2, John E. Johnson 3 and Gino Cingolani 4 1 Department of Biological Sciences, Purdue University,
Table S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1.
Table S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1. PDZK1 constru cts Amino acids MW [kda] KD [μm] PEPT2-CT- FITC KD [μm] NHE3-CT- FITC KD [μm] PDZK1-CT-
Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space
Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space Pablo Gainza CPS 296: Topics in Computational Structural Biology Department of Computer
Introduction to Comparative Protein Modeling. Chapter 4 Part I
Introduction to Comparative Protein Modeling Chapter 4 Part I 1 Information on Proteins Each modeling study depends on the quality of the known experimental data. Basis of the model Search in the literature
Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets
Supporting information Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets Wan-Na Chen, Christoph Nitsche, Kala Bharath Pilla, Bim Graham, Thomas
Template-Based Modeling of Protein Structure
Template-Based Modeling of Protein Structure David Constant Biochemistry 218 December 11, 2011 Introduction. Much can be learned about the biology of a protein from its structure. Simply put, structure
CRYO-EM GUIDED DE NOVO PROTEIN FOLDING. Steffen Lindert. Dissertation. Submitted to the Faculty of the. Graduate School of Vanderbilt University
CRYO-EM GUIDED DE NOVO PROTEIN FOLDING By Steffen Lindert Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment of the requirements for the degree
Presenter: She Zhang
Presenter: She Zhang Introduction Dr. David Baker Introduction Why design proteins de novo? It is not clear how non-covalent interactions favor one specific native structure over many other non-native
Dihedral Angles. Homayoun Valafar. Department of Computer Science and Engineering, USC 02/03/10 CSCE 769
Dihedral Angles Homayoun Valafar Department of Computer Science and Engineering, USC The precise definition of a dihedral or torsion angle can be found in spatial geometry Angle between to planes Dihedral
Nature Structural and Molecular Biology: doi: /nsmb.2938
Supplementary Figure 1 Characterization of designed leucine-rich-repeat proteins. (a) Water-mediate hydrogen-bond network is frequently visible in the convex region of LRR crystal structures. Examples
Truncating Spy s unstructured tails does not dramatically decrease chaperone activity in vivo or in vitro.
Supplementary Figure 1 Truncating Spy s unstructured tails does not dramatically decrease chaperone activity in vivo or in vitro. (a) Overexpression of Spy increases the steady state level of the unstable
Programme Last week s quiz results + Summary Fold recognition Break Exercise: Modelling remote homologues
Programme 8.00-8.20 Last week s quiz results + Summary 8.20-9.00 Fold recognition 9.00-9.15 Break 9.15-11.20 Exercise: Modelling remote homologues 11.20-11.40 Summary & discussion 11.40-12.00 Quiz 1 Feedback
Supplementary Information: Long range allosteric regulation of the human 26S proteasome by 20S proteasome-targeting cancer drugs
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Supplementary Information: Long range allosteric regulation of the human 26S proteasome by 20S proteasome-targeting cancer drugs
Supporting Information
Supporting Information Micelle-Triggered b-hairpin to a-helix Transition in a 14-Residue Peptide from a Choline-Binding Repeat of the Pneumococcal Autolysin LytA HØctor Zamora-Carreras, [a] Beatriz Maestro,
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11524 Supplementary discussion Functional analysis of the sugar porter family (SP) signature motifs. As seen in Fig. 5c, single point mutation of the conserved
CMPS 6630: Introduction to Computational Biology and Bioinformatics. Tertiary Structure Prediction
CMPS 6630: Introduction to Computational Biology and Bioinformatics Tertiary Structure Prediction Tertiary Structure Prediction Why Should Tertiary Structure Prediction Be Possible? Molecules obey the
Protein Structure Prediction, Engineering & Design CHEM 430
Protein Structure Prediction, Engineering & Design CHEM 430 Eero Saarinen The free energy surface of a protein Protein Structure Prediction & Design Full Protein Structure from Sequence - High Alignment
Supplementary Figure 1 Crystal packing of ClR and electron density maps. Crystal packing of type A crystal (a) and type B crystal (b).
Supplementary Figure 1 Crystal packing of ClR and electron density maps. Crystal packing of type A crystal (a) and type B crystal (b). Crystal contacts at B-C loop are magnified and stereo view of A-weighted
SUPPLEMENTARY INFORMATION. doi: /nature07461
Figure S1 Electrophysiology. a ph-activation of. Two-electrode voltage clamp recordings of Xenopus oocytes expressing in comparison to waterinjected oocytes. Currents were recorded at 40 mv. The ph of
Protein Structure Prediction
Protein Structure Prediction Michael Feig MMTSB/CTBP 2006 Summer Workshop From Sequence to Structure SEALGDTIVKNA Ab initio Structure Prediction Protocol Amino Acid Sequence Conformational Sampling to
SUPPLEMENTARY INFORMATION
Supplementary materials Figure S1 Fusion protein of Sulfolobus solfataricus SRP54 and a signal peptide. a, Expression vector for the fusion protein. The signal peptide of yeast dipeptidyl aminopeptidase
SUPPLEMENTARY INFORMATION
Fig. 1 Influences of crystal lattice contacts on Pol η structures. a. The dominant lattice contact between two hpol η molecules (silver and gold) in the type 1 crystals. b. A close-up view of the hydrophobic
Template Free Protein Structure Modeling Jianlin Cheng, PhD
Template Free Protein Structure Modeling Jianlin Cheng, PhD Professor Department of EECS Informatics Institute University of Missouri, Columbia 2018 Protein Energy Landscape & Free Sampling http://pubs.acs.org/subscribe/archive/mdd/v03/i09/html/willis.html
Supporting Online Material for
www.sciencemag.org/cgi/content/full/309/5742/1868/dc1 Supporting Online Material for Toward High-Resolution de Novo Structure Prediction for Small Proteins Philip Bradley, Kira M. S. Misura, David Baker*
SUPPLEMENTARY INFORMATION
DOI: 10.1038/NCHEM.1290 Metal-directed, chemically tunable assembly of one-, two- and threedimensional crystalline protein arrays 1 2 1 1 1,3 Jeffrey D. Brodin 1, X. I. Ambroggio 2, Chunyan Tang 1, Kristin
SUPPLEMENTARY INFORMATION
Dph2 SeMet (iron-free) # Dph2 (iron-free) Dph2-[4Fe-4S] Data collection Space group P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell dimensions a, b, c (Å) 58.26, 82.08, 160.42 58.74, 81.87, 160.01 55.70, 80.53,
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Jan 28, 2019 11:10 AM EST PDB ID : 6A5H Title : The structure of [4+2] and [6+4] cyclase in the biosynthetic pathway of unidentified natural product Authors
Supplementary Materials for
advances.sciencemag.org/cgi/content/full/3/6/e1700147/dc1 Supplementary Materials for Ribosome rearrangements at the onset of translational bypassing Xabier Agirrezabala, Ekaterina Samatova, Mariia Klimova,
Towards De Novo Folding of Protein Structures from Cryo-EM 3D Images at Medium Resolutions
Towards De Novo Folding of Protein Structures from Cryo-EM 3D Images at Medium Resolutions Jing He * and Dong Si Department of Computer Science Old Dominion University Norfolk, VA * jhe@cs.odu.edu Abstract
Diphthamide biosynthesis requires a radical iron-sulfur enzyme. Pennsylvania State University, University Park, Pennsylvania 16802, USA
Diphthamide biosynthesis requires a radical iron-sulfur enzyme Yang Zhang, 1,4 Xuling Zhu, 1,4 Andrew T. Torelli, 1 Michael Lee, 2 Boris Dzikovski, 1 Rachel Koralewski, 1 Eileen Wang, 1 Jack Freed, 1 Carsten
Nature Methods: doi: /nmeth Supplementary Figure 1. Atomic models in cryo-em maps.
Supplementary Figure 1 Atomic models in cryo-em maps. (a) Two alpha (blue) and two beta (green) subunits of the T20S proteasome are shown as cartoon tubes fitted in a 3.2 Å potential map at isolevel 0.25
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 10:24 pm GMT PDB ID : 1A30 Title : HIV-1 PROTEASE COMPLEXED WITH A TRIPEPTIDE INHIBITOR Authors : Louis, J.M.; Dyda, F.; Nashed, N.T.; Kimmel,
Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6
Supplementary Information for: Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6 Yawei Dai 1, 2, Markus Seeger 3, Jingwei Weng 4, Song Song 1, 2, Wenning Wang 4, Yan-Wen 1, 2,
Supplemental Figure and Movie Legends Figure S1. Time course experiments on the thermal stability of apo AT cpn-α by native PAGE (related to Figure 2B). The samples were heated, respectively, to (A) 45
A new prediction strategy for long local protein. structures using an original description
Author manuscript, published in "Proteins Structure Function and Bioinformatics 2009;76(3):570-87" DOI : 10.1002/prot.22370 A new prediction strategy for long local protein structures using an original
Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization
Biophysical Journal Volume 101 November 2011 2525 2534 2525 Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization Dong Xu and Yang Zhang
Supplementary information for cloud computing approaches for prediction of ligand binding poses and pathways
Supplementary information for cloud computing approaches for prediction of ligand binding poses and pathways Morgan Lawrenz 1, Diwakar Shukla 1,2 & Vijay S. Pande 1,2 1 Department of Chemistry, Stanford
Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein
Acta Cryst. (2015). D71, 274-282, doi:10.1107/s1399004714025243 Supporting information Volume 71 (2015) Supporting information for article: Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11744 Supplementary Table 1. Crystallographic data collection and refinement statistics. Wild-type Se-Met-BcsA-B SmCl 3 -soaked EMTS-soaked Data collection Space
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Jan 17, 2019 09:42 AM EST PDB ID : 6D3Z Title : Protease SFTI complex Authors : Law, R.H.P.; Wu, G. Deposited on : 2018-04-17 Resolution : 2.00 Å(reported)
A dynamic interaction process between KaiA and KaiC is critical to
A dynamic interaction process between KaiA and KaiC is critical to the cyanobacterial circadian oscillator Pei Dong 1,2, Ying Fan 2, Jianqiang Sun 3, Mengting Lv 2, Ming Yi 4, Xiao Tan 1,2, Sen Liu 1,2,*
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Identification of the ScDcp2 minimal region interacting with both ScDcp1 and the ScEdc3 LSm domain. Pull-down experiment of untagged ScEdc3 LSm with various ScDcp1-Dcp2-His 6 fragments.
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 13, 2018 04:03 pm GMT PDB ID : 5NMJ Title : Chicken GRIFIN (crystallisation ph: 6.5) Authors : Ruiz, F.M.; Romero, A. Deposited on : 2017-04-06 Resolution
Automated identification of functional dynamic contact networks from X-ray crystallography
1 Automated identification of functional dynamic contact networks from X-ray crystallography Henry van den Bedem, Gira Bhabha, Kun Yang, Peter E. Wright and James S. Fraser Supplementary Figure 1 Supplementary
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 06:13 pm GMT PDB ID : 5G5C Title : Structure of the Pyrococcus furiosus Esterase Pf2001 with space group C2221 Authors : Varejao, N.; Reverter,
SUPPLEMENTARY INFORMATION
doi:10.1038/nature10955 Supplementary Figures Supplementary Figure 1. Electron-density maps and crystallographic dimer structures of the motor domain. (a f) Stereo views of the final electron-density maps
Supplemental Data SUPPLEMENTAL FIGURES
Supplemental Data CRYSTAL STRUCTURE OF THE MG.ADP-INHIBITED STATE OF THE YEAST F 1 C 10 ATP SYNTHASE Alain Dautant*, Jean Velours and Marie-France Giraud* From Université Bordeaux 2, CNRS; Institut de
Part 8 Working with Nucleic Acids
Part 8 Working with Nucleic Acids http://cbm.msoe.edu/newwebsite/learntomodel Introduction Most Protein Databank files loaded into the CBM's Jmol Design Environment include protein structures and small
Overview. The peptide bond. Page 1
Overview Secondary structure: the conformation of the peptide backbone The peptide bond, steric implications Steric hindrance and sterically allowed conformations. Ramachandran diagrams Side chain conformations
Computational engineering of cellulase Cel9A-68 functional motions through mutations in its linker region. WT 1TF4 (crystal) -90 ERRAT PROVE VERIFY3D
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 218 Supplementary Material: Computational engineering of cellulase Cel9-68 functional
07/30/2012 Rose=a Conference. Principle for designing! ideal protein structures! Nobuyasu & Rie Koga University of Washington
07/30/2012 Rose=a Conference Principle for designing! ideal protein structures! Nobuyasu & Rie Koga University of Washington Naturally occurring protein structures are complicated Functional site or junks
Useful background reading
Overview of lecture * General comment on peptide bond * Discussion of backbone dihedral angles * Discussion of Ramachandran plots * Description of helix types. * Description of structures * NMR patterns
CMPS 3110: Bioinformatics. Tertiary Structure Prediction
CMPS 3110: Bioinformatics Tertiary Structure Prediction Tertiary Structure Prediction Why Should Tertiary Structure Prediction Be Possible? Molecules obey the laws of physics! Conformation space is finite
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Jan 14, 2019 11:10 AM EST PDB ID : 6GYW Title : Crystal structure of DacA from Staphylococcus aureus Authors : Tosi, T.; Freemont, P.S.; Grundling, A. Deposited
Protein Folding by Robotics
Protein Folding by Robotics 1 TBI Winterseminar 2006 February 21, 2006 Protein Folding by Robotics 1 TBI Winterseminar 2006 February 21, 2006 Protein Folding by Robotics Probabilistic Roadmap Planning
Nature Structural and Molecular Biology: doi: /nsmb Supplementary Figure 1. Experimental approach for enhancement of unbiased Fo Fc maps.
Supplementary Figure 1 Experimental approach for enhancement of unbiased Fo Fc maps. a, c, Unbiased Fo-Fc maps of the Tth 70S post-catalysis complex at 2.55 Å resolution with (a) or without (c) bulk solvent
Protein structure prediction. CS/CME/BioE/Biophys/BMI 279 Oct. 10 and 12, 2017 Ron Dror
Protein structure prediction CS/CME/BioE/Biophys/BMI 279 Oct. 10 and 12, 2017 Ron Dror 1 Outline Why predict protein structure? Can we use (pure) physics-based methods? Knowledge-based methods Two major
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 14, 2018 02:00 pm GMT PDB ID : 3RRQ Title : Crystal structure of the extracellular domain of human PD-1 Authors : Lazar-Molnar, E.; Ramagopal, U.A.; Nathenson,
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Cryo-EM structure and model of the C. thermophilum 90S preribosome. a, Gold standard FSC curve showing the average resolution of the 90S preribosome masked and unmasked (left). FSC
FlexPepDock In a nutshell
FlexPepDock In a nutshell All Tutorial files are located in http://bit.ly/mxtakv FlexPepdock refinement Step 1 Step 3 - Refinement Step 4 - Selection of models Measure of fit FlexPepdock Ab-initio Step
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 08:34 pm GMT PDB ID : 1RUT Title : Complex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain Authors : Deane, J.E.; Ryan, D.P.; Maher, M.J.;
Acta Crystallographica Section D
Supporting information Acta Crystallographica Section D Volume 70 (2014) Supporting information for article: Structural characterization of the virulence factor Nuclease A from Streptococcus agalactiae
Full wwpdb/emdatabank EM Map/Model Validation Report i
Full wwpdb/emdatabank EM Map/Model Validation Report i Sep 25, 2018 07:01 PM EDT PDB ID : 6C0V EMDB ID: : EMD-7325 Title : Molecular structure of human P-glycoprotein in the ATP-bound, outwardfacing conformation
GDR1 photometry. CU5/DPCI team
GDR1 photometry CU5/DPCI team What is, or isn't included GDR1 only provides G mean flux and error Derived mean magnitude, all entries Zero point used is in Vega system Zero point for AB system also available
Assessing the potential of atomistic molecular dynamics simulations to probe reversible. protein-protein recognition and binding
Supporting information for Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding Luciano A. Abriata and Matteo Dal Peraro Laboratory
SUPPLEMENTARY FIGURES. Structure of the cholera toxin secretion channel in its. closed state
SUPPLEMENTARY FIGURES Structure of the cholera toxin secretion channel in its closed state Steve L. Reichow 1,3, Konstantin V. Korotkov 1,3, Wim G. J. Hol 1$ and Tamir Gonen 1,2$ 1, Department of Biochemistry
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 10, 2018 01:44 am GMT PDB ID : 1MWP Title : N-TERMINAL DOMAIN OF THE AMYLOID PRECURSOR PROTEIN Authors : Rossjohn, J.; Cappai, R.; Feil, S.C.; Henry,
Supplementary Figure 1
Supplementary Figure 1 The correlation of n-score cutoff and FDR in both CID-only and CID-ETD fragmentation strategies. A bar diagram of different n-score thresholds applied in the search, plotted against
Physiochemical Properties of Residues
Physiochemical Properties of Residues Various Sources C N Cα R Slide 1 Conformational Propensities Conformational Propensity is the frequency in which a residue adopts a given conformation (in a polypeptide)
Prediction and refinement of NMR structures from sparse experimental data
Prediction and refinement of NMR structures from sparse experimental data Jeff Skolnick Director Center for the Study of Systems Biology School of Biology Georgia Institute of Technology Overview of talk
Protein quality assessment
Protein quality assessment Speaker: Renzhi Cao Advisor: Dr. Jianlin Cheng Major: Computer Science May 17 th, 2013 1 Outline Introduction Paper1 Paper2 Paper3 Discussion and research plan Acknowledgement