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Sample search results for: ab initio folding

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1 Protein Structure Analysis Iosif Vaisman
 

Summary:  molecular simulation · Knowledge-based methods: homology modeling fold recogniion Ab initio Methods... Methods · Ab initio methods: solution of a protein folding problem search in conformational space · Energy... Protein Structure Analysis Iosif Vaisman 2009 BINF ...

  

Source: Vaisman, Iosif - Bioinformatics and Computational Biology Program, School of Computational Sciences, George Mason University

 

Collection: Biotechnology

 
2 Present and Future Prospects of Protein Structure Prediction Sung-Joon Park Department of Chemistry, Faculty of Science, Kobe University
 

Summary:  ://theory.chem.sci.kobe-u.ac.jp/ keywords: protein structure prediction, comparative modeling, fold recognition, ab initio, CASP 1. 40 X... 03] § 3 PSI-BLAST PSI-BLAST IMPALA[Schaffer 99] [Wang 04] 3 2 § 1 ab initio ab initio ...

  

Source: Takada, Shoji - Department of Biophysics, Kyoto University

 

Collection: Chemistry ; Biotechnology

 
3 CS 374 Abhishek Rathod Prof. Serafim Batzoglou 12/02/2005
 

Summary:  .1146/annurev.biophys.30.1.173 Abstract: Homology-based comparative modeling, Fold recognition and Ab initio... CS 374 Abhishek Rathod Prof. Serafim Batzoglou 12/02/2005 Ab initio protein structure prediction... reviews features of current ab ...

  

Source: Batzoglou, Serafim - Department of Computer Science, Stanford University

 

Collection: Biotechnology ; Computer Technologies and Information Sciences

 
4 University of Maryland Symposium on Theoretical Chemistry 15 April 2009, 9:00 AM
 

Summary:  Speakers Joel Bowman (Emory University) "Ab initio-based full dimensional water dimer and trimer potentials... and on towards a general ab initio potential for water" Kenneth Jordan (University of Pittsburgh) Millard... (Tulane) Devarajan Thirumalai (University of Maryland) "Folding in ...

  

Source: Krylov, Anna I. - Department of Chemistry, University of Southern California

 

Collection: Chemistry

 
5 Electronic Excitations in Carbon Nanostructures: Building-Block Approach
 

Summary:  ZF q | = 0.18 1/Å q|| = 0.23 1/Å q R. Hambach Building-Block Approach #12;Ab-Initio vs. Zone-Folding... -Block Approach #12;Ab-Initio Calculations for Graphene full ab-initio calculations 1. ground-state calculation... -code: www.dp-code.org; V. Olevano, et al., unpublished. R. Hambach Building-Block ...

  

Source: Botti, Silvana - Laboratoire des Solides Irradiés, École Polytechnique

 

Collection: Materials Science

 
6 Nasir Mahmood1, TJ Brunette2 and Oliver Brock1 1 -Robotics and Biology Laboratory, Technical University Berlin, Germany
 

Summary:  adaptive exploration-exploitation mechanism. An Attempt to Unite Homology Modeling and Ab Initio Structure... Prediction Homologs Fragments PDB Amino Acids MotifsFolds BEETS Strategy ­ Adaptive Balancing of Exploitation... will be increased. Homologs Fragments PDB Amino Acid MotifsFolds exploitation ...

  

Source: 

 

Collection: Engineering ; Computer Technologies and Information Sciences

 
7 Ab Initio Protein Structure Prediction via a Combination of Threading, Lattice Folding, Clustering, and Structure
 

Summary:  Ab Initio Protein Structure Prediction via a Combination of Threading, Lattice Folding, Clustering... and new fold categories. For a few targets (T0110 is probably the best example), the ab initio method... , with fold selection being more ...

  

Source: Kihara, Daisuke - Department of Biological Sciences, Purdue University; Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Biology and Medicine ; Biotechnology ; Chemistry

 
8 Collective Excitations in Nanostructures: Towards Spatially-Resolved EELS
 

Summary:  ] q Angular-Resolved EELS: SWCNTs Building-Block Approach #12;Ab-Initio vs. Zone-Folding: CNT(9,9) on... || = 0.23 1/Å q Angular-Resolved EELS: SWCNTs Building-Block Approach #12;Ab-Initio vs. Zone-Folding: CNT... -Mode Decomposition Spatially-Resolved EELS: Graphene Towards Ab-Initio ...

  

Source: Botti, Silvana - Laboratoire des Solides Irradiés, École Polytechnique

 

Collection: Materials Science

 
9 An Overview of Protein Structure Prediction: From Homology to Ab Initio
 

Summary:  , comparative modeling, threading or fold recognition, and Ab Initio prediction, is described. The accuracy... ) homology modeling, 2) threading or fold recognition, and 3) Ab Initio. Essentially, the classification... An Overview of Protein Structure Prediction: From ...

  

Source: Bejerano, Gill - Departments of Computer Science & Developmental Biology, Stanford University

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
10 The Role of Structure, Energy Landscape, Dynamics, and Allostery in the Enzymatic Function of Myoglobin
 

Summary:  in cardiac and skeletal muscle. Our model is supported by an ab initio QM model of CO binding to myoglobin... , in the folded as well as a partially unfolded state. The allostery is implied by the behavior of the taxonomic

  

Source: Groves, John T. - Department of Chemistry, Princeton University

 

Collection: Chemistry

 
11 A review of recent advances in ab initio protein folding by the Folding@home project
 

Summary:  A review of recent advances in ab initio protein folding by the Folding@home project William Ito... Abstract The Folding@home project harnesses a volunteer distributed computing network to perform ab initio... client and its use in ...

  

Source: Bejerano, Gill - Departments of Computer Science & Developmental Biology, Stanford University

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
12 Ab initio Protein Structure Prediction Using Pathway Models Xin Yuan, Yu Shao, and Christopher Bystroff
 

Summary:  . (2002). Ab initio folding of multiple-chain proteins. Pac Symp Biocomput, 601-12. Shao, Y. & Bystroff, C... 1 1 Ab initio Protein Structure Prediction Using Pathway Models Xin Yuan, Yu Shao, and Christopher... Bystroff Department of Biology, Rensselaer Polytechnic Institute, Troy, ...

  

Source: Bystroff, Chris - Department of Biology, Rensselaer Polytechnic Institute

 

Collection: Biotechnology ; Biology and Medicine

 
13 Prorein Science (1998). 7:1998-2003.CambridgeUniversityPress.Printed in the USA Copyright 0 1998TheProteinSociety
 

Summary:  these restraints resulted in an average coordinate RMS error of 4.38 A. Keywords: ab initio folding; distance... . So-called "ab initio" computationalap- proaches seek the overall fold of the polypeptide, often... -square (RMS) from the native BPTl ...

  

Source: Samudrala, Ram - Department of Microbiology, University of Washington at Seattle

 

Collection: Biotechnology ; Biology and Medicine

 
14 Dislocation core energies and core fields from first principles Emmanuel Clouet,1, 2
 

Summary:  or if the stress ex- perienced by the dislocation also obeys this 3-fold sym- metry. The ab initio calculations... Lille 1, 59655 Villeneuve d'Ascq, France (Dated: February 9, 2009) Ab initio calculations in bcc iron... modeling thus better reproduces the atom displacements observed in ...

  

Source: Ecole Polytechnique, Centre de mathématiques

 

Collection: Mathematics

 
15 All-Atom Ab Initio Folding of a Diverse Set of Proteins
 

Summary:  Structure Article All-Atom Ab Initio Folding of a Diverse Set of Proteins Jae Shick Yang,1 William... problems in bio- physics. Here, we show successful all-atom ab initio folding of a representative diverse... a few crucial energetic terms. INTRODUCTION ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine

 
16 Protein Science (1998), 7: 1998-2003. Cambridge University Press. Printed in the USA. Copyright 1998 The Protein Society
 

Summary:  in an average coordinate RMS error of 4.38 Å. Keywords: ab initio folding; distance geometry; energy functions... . In the context of more recent ab initio folding studies, these methods have harnessed inter-atomic distance... collected from an ...

  

Source: Huang, Enoch S. - Bioinformatics Program, Boston University; Ponder, Jay - Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis

 

Collection: Biology and Medicine ; Biotechnology

 
17 Recursive Protein Structure Jianlin Cheng, PhD
 

Summary:  ;Template-Free (Ab Initio) Modeling Dill & Chan, 1997 Protein Structure Space Native Structure #12;Template... Structure Template-based modeling (GDT-TS = 0.34) Template-based + Ab Initio (GDT-TS = 0.39) #12;Native... Structure Template-based modeling (GDT-TS = 0.34) Template-based + ...

  

Source: Cheng, Jianlin Jack - Department of Computer Science, University of Missouri-Columbia

 

Collection: Computer Technologies and Information Sciences

 
18 Thermodynamic processes of Si-interstitial clusters Jeongnim Kim,1
 

Summary:  range of interatomic potentials, from classical to ab initio potentials. Parallel-replica simulations... and tran- sition paths captured by parallel-replica simulations are used as the inputs for ab initio total... to extended {311} defects is derived from the ab ...

  

Source: Wilkins, John - Department of Physics, Ohio State University

 

Collection: Materials Science ; Physics

 
19 roteins are the workhorses of life. These polymers, comprised of 20 natu-
 

Summary:  prediction: homology modeling, threading, and ab initio folding. In homology modeling,6 the query sequence... structure must already exist. With ab initio fold- ing, we attempt to fold a protein from a random... threading algorithm for protein ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine

 
20 22842294 Nucleic Acids Research, 2008, Vol. 36, No. 7 Published online 20 February 2008 doi:10.1093/nar/gkn064
 

Summary:  .1093/nar/gkn064 Empirical comparison of ab initio repeat finding programs Surya Saha1,2,3 , Susan Bridges1... repetitive elements in an ab initio manner, i.e. without using prior sequence data. Here we present... the results of side-by-side evaluations of six of the most widely used ab ...

  

Source: Ray, David - Department of Biochemistry and Molecular Biology, Mississippi State University

 

Collection: Environmental Sciences and Ecology


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21 INSTITUTE OF PHYSICS PUBLISHING MEASUREMENT SCIENCE AND TECHNOLOGY Meas. Sci. Technol. 16 (2005) 296301 doi:10.1088/0957-0233/16/1/039
 

Summary:  ) 296­301 doi:10.1088/0957-0233/16/1/039 High-throughput and data mining with ab initio methods Dane... 2004 Published 16 December 2004 Online at stacks.iop.org/MST/16/296 Abstract Accurate ab initio methods... in computer speed and ab initio algorithms have now ...

  

Source: Curtarolo, Stefano - Department of Mechanical Engineering and Materials Science, Duke University

 

Collection: Materials Science

 
22 W354W356 Nucleic Acids Research, 2007, Vol. 35, Web Server issue doi:10.1093/nar/gkm390
 

Summary:  -based and ab initio methods. The preli- minary version of the server was ranked among the top domain prediction... . These methods can be roughly classified into four categories: template-based methods (6­10), ab initio (template... -free) methods (11­22), the hybrid approach combining template-based and ...

  

Source: Cheng, Jianlin Jack - Department of Computer Science, University of Missouri-Columbia

 

Collection: Computer Technologies and Information Sciences

 
23 Kataura plot based on GWA graphene dispersion Mototeru Oba1)
 

Summary:  with ab-initio calculation such as local density approximation (LDA) and GW approximation (GWA... ways to calculate the plot: one is to calculate SWNT energy band directly; another is to use zone-folding... ), a comprehensive technique to compensate the curvature effect on zone-folding method (Fig. 1) is desired. Here

  

Source: Maruyama, Shigeo - Department of Mechanical Engineering, University of Tokyo

 

Collection: Materials Science

 
24 Gilles Zerah Large scale parallel ab initio electronic structure
 

Summary:  Gilles Z´erah Large scale parallel ab initio electronic structure calculations with the LOBPCG... ¸cois Bottin St´ephane Le Roux Andrew Knyazev We present an implementation in the ab initio plane-wave code... . Leroux, A. Knyazev, G. Zerah, Large scale ab initio ...

  

Source: Knyazev, Andrew - Department of Mathematics, University of Colorado at Denver

 

Collection: Mathematics

 
25 Ab Initio Prediction of the Three-Dimensional Structure of a De Novo Designed Protein: A Double-Blind Case Study
 

Summary:  models. Recently, a novel 4-stage ab initio approach, ASTRO- FOLD, was introduced for the structure... elsewhere.7 It must be emphasized that ASTRO-FOLD is an entirely ab initio method. Thus, for the current... initio prediction of the structure ...

  

Source: Hecht, Michael H. - Departments of Chemistry & Molecular Biology, Princeton University

 

Collection: Chemistry ; Biotechnology

 
26 Band gap engineering in amorphous AlxGa1xN: Experiment and ab initio calculations
 

Summary:  of three-fold defects in our ab initio calculations decreases with increasing Al composition for the five... Band gap engineering in amorphous AlxGa1ÀxN: Experiment and ab initio calculations Hong Chen... 3.27 eV a-GaN to 5.95 eV a-AlN have been synthesized. Ab ...

  

Source: Drabold, David - Department of Physics and Astronomy, Ohio University

 

Collection: Materials Science ; Physics

 
27 TOUCHSTONE: A Unified Approach to Protein Structure Jeffrey Skolnick,1* Yang Zhang,1
 

Summary:  that spans the range from homology modeling to ab initio folding to all protein targets in CASP5. Using our... at least weakly threading templates are pooled and incorporated into ab initio folding. Often, TOUCHSTONE... analogous templates. When ...

  

Source: Kihara, Daisuke - Department of Biological Sciences, Purdue University; Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Biology and Medicine ; Biotechnology ; Chemistry

 
28 Title of article: Scoring functions for ab initio protein structure prediction Suggested running head: Scoring functions for ab initio methods
 

Summary:  energy functions, and place an emphasis on functions tailored for ab initio folding, although much... , to build side-chain conformations. However, in threading and ab initio folding, one is primarily concerned... with capturing the overall fold, ...

  

Source: Samudrala, Ram - Department of Microbiology, University of Washington at Seattle

 

Collection: Biotechnology ; Biology and Medicine

 
29 Accuracy of Side-Chain Prediction Upon Near-Native Protein Backbones Generated by Ab Initio
 

Summary:  Accuracy of Side-Chain Prediction Upon Near-Native Protein Backbones Generated by Ab Initio Folding... The ab initio folding problem can be divided into two sequential tasks of approximately equal... backbones on side-chain prediction for folds ...

  

Source: California at Davis, University of - Computer Science Department, Computer Science Theory Laboratory; Huang, Enoch S. - Bioinformatics Program, Boston University; Levitt, Michael - Department of Structural Biology, Stanford University; Ponder, Jay - Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis

 

Collection: Biology and Medicine ; Biotechnology ; Computer Technologies and Information Sciences

 
30 images/logoetsf Introduction Electron Energy Loss Spectroscopy Applications: Nanotubes and Graphene Perspectives
 

Summary:  Perspectives Ab Initio calculations of electronic excitations Carbon Nanotubes and Graphene layer systems... Theoretical Spectroscopy Facility (ETSF) Strasbourg, 27 August 2008 Ab Initio calculations of electronic... 3 Applications: Nanotubes and Graphene 4 Perspectives Ab ...

  

Source: Botti, Silvana - Laboratoire des Solides Irradiés, École Polytechnique

 

Collection: Materials Science

 
31 Ab initio potentials for the S,,3 Pj...rare gas dimers: Implementation
 

Summary:  Ab initio potentials for the S,,3 Pj...­rare gas dimers: Implementation for elastic and inelastic... states are calculated ab initio using an unrestricted CCSD T level of theory and extended correlation... , whose validity is verified by the direct ab initio ...

  

Source: Krems, Roman - Department of Chemistry, University of British Columbia

 

Collection: Physics ; Chemistry

 
32 This journal is c The Royal Society of Chemistry 2011 Mol. BioSyst. Cite this: DOI: 10.1039/c1mb05207a
 

Summary:  ://mendel.imp.ac.at/METHODS/seg.server.html Ab initio method GlobPlot http://globplot.embl.de/ Ab initio method FoldIndex http... into four different categories: (1) ab initio, or sequence only, (2) clustering, (3) template based and (4... the ...

  

Source: Cheng, Jianlin Jack - Department of Computer Science, University of Missouri-Columbia

 

Collection: Computer Technologies and Information Sciences

 
33 Ab initio investigation of barium-scandium-oxygen coatings on tungsten for electron emitting cathodes
 

Summary:  Ab initio investigation of barium-scandium-oxygen coatings on tungsten for electron emitting... functional theory (DFT) based ab initio modeling is used to explore the stability and work function of Bax... be calculated easily using ab initio calculations and fitting ...

  

Source: Wisconsin at Madison, University of - Department of Engineering Physics, Computational Materials Group

 

Collection: Fission and Nuclear Technologies ; Materials Science

 
34 Predicting Interresidue Contacts Using Templates and Pathways
 

Summary:  potentials then were used to evaluate these templates. An ab initio method based on the target contact... and ab initio methods were combined to produce accurate, protein-like contact maps. Pathways sometimes... targets are dis- cussed. Also included is a brief update on the quality of fully automated ...

  

Source: Bystroff, Chris - Department of Biology, Rensselaer Polytechnic Institute

 

Collection: Biotechnology ; Biology and Medicine

 
35 Nanoscience on High Performance Computers: From Methods to Codes to Applications
 

Summary:  , surface effects and no dislocations #12;Computational challenges (larger nanostructures) ·Ab initio method... ) method Ab initio Method ·Effective mass method Challenge for computational nanoscience. Ab initio... elements and reliability New methodology and ...

  

Source: Lawrence Berkeley National Laboratory, Computational Research Division, Distributed Systems Department, Data Intensive Distributed Computing Group

 

Collection: Computer Technologies and Information Sciences

 
36 Benchmarking of TASSER in the Ab Initio Limit Jose M. Borreguero and Jeffrey Skolnick*
 

Summary:  . Proteins 2007;68:48­56. VVC 2007 Wiley-Liss, Inc. Key words: ab initio folding; protein folding; pro- tein... is that the ab initio folding of helical proteins was more successful than for proteins containing b sheets.4... /Refinement) ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine

 
37 10.1261/rna.894608Access the most recent version at doi: 2008 14: 1164-1173; originally published online May 2, 2008;RNA
 

Summary:  , Natalia E. Broude and Nikolay V. structure prediction to folding mechanisms Ab initio RNA folding... .rnajournal.orgDownloaded from #12;Ab initio RNA folding by discrete molecular dynamics: From structure prediction to ...

  

Source: Dokholyan, Nikolay V. - Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill

 

Collection: Physics ; Biology and Medicine

 
38 Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations
 

Summary:  Folding processes of the B domain of protein A to the native state observed in all-atom ab initio... mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite... of the best nativelike structures from previous ...

  

Source: Zhou, Yaoqi - School of Informatics, Indiana University

 

Collection: Biology and Medicine

 
39 Tara Watkins Biochem 218
 

Summary:  resolution ab initio models. Biopolymers 70:575-584. Martin, J. 1998. Protein folding assisted by Gro... of the target protein is based on the structure of these previously resolved template proteins. Ab initio... drugs. In the case of ab initio ...

  

Source: Bejerano, Gill - Departments of Computer Science & Developmental Biology, Stanford University

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
40 CASP AND CAFASP EXPERIMENTS AND THEIR FINDINGSED1
 

Summary:  , fold recognition (also known as threading) and ab initio, the latter having been reclassified as "new... in earlier CASPs as ab initio fold prediction, but was renamed in CASP4 to better define the current... (ab initio)? ...

  

Source: Bourne, Philip E. - San Diego Supercomputer Center, University of California at San Diego

 

Collection: Biology and Medicine


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41 BIOCHEM218: Computational Molecular Biology Professor Douglas Brutlag
 

Summary:  Structure Prediction via Ab initio) Protein structure prediction is distinct from protein folding problem... (ab initio), as folding problem is concerned with modeling and predicting the three... , and the tertiary structure is modeled using the algorithms discussed ...

  

Source: Bejerano, Gill - Departments of Computer Science & Developmental Biology, Stanford University

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
42 Multi-Laser-Beam Open-Atmosphere Surface Coating Techniques Based on Precursor Excitation, Photodissociation and Controlled Cooling
 

Summary:  .) for fast diamond growth; (2) Theoretically (ab initio, molecular dynamics and continuum models) investigate... -Lung Tsai, "Calculation of Thermophysical Properties of CO2 Gas Using an Ab Initio Potential Model... , "Ab Initio Calculations of Infrared Absorption ...

  

Source: Ragsdell, Kenneth M. - Design Engineering Center, University of Missouri-Rolla

 

Collection: Engineering

 
43 Protein Structure Prediction Jayanthi Sourirajan
 

Summary:  using different algorithms and different methods- homology, fold recognition and ab-initio. Subsequently... recognition/homology 20-30% >75% 2-5Ao Easy Fold recognition <20% >50% 3-10Ao Moderate Ab-initio <5 0 5-20Ao... is predicted using Ab-initio prediction. #12;Secondary ...

  

Source: Bejerano, Gill - Departments of Computer Science & Developmental Biology, Stanford University

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
44 Probabilistic Graphical Model for Protein Structure Prediction If we know the primary sequence of a protein, can we predict its three
 

Summary:  threading/homology modeling) and templatefree modeling (i.e., ab initio folding). Templatebased modeling

  

Source: Jackson, Daniel - Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT)

 

Collection: Computer Technologies and Information Sciences

 
45 Joshua Schrier Lin-Wang Wang
 

Summary:  , such as semiconductor nanocrystals, an approximate ab initio potential may be constructed by patching together local... , and the eigenvalues determined using the folded spectrum method for a few band-edge states. In this talk, I

  

Source: Lee, Jason R. - Data Intensive Distributed Computing Group, Distributed Systems Department, National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory

 

Collection: Computer Technologies and Information Sciences

 
46 J. Mol. Biol. (1996) 264, 11641179 How to Derive a Protein Folding Potential? A New
 

Summary:  decoys is still not strong enough to make the potential useful for ab initio folding. Our results suggest... and ab initio folding. The results of numerous tests by many groups (see the comprehensive analysis... a decent job in fold recognition, ...

  

Source: Mirny, Leonid - Harvard-MIT Division of Health Sciences and Technology & Department of Physics, Massachusetts Institute of Technology (MIT)

 

Collection: Biotechnology ; Biology and Medicine ; Physics

 
47 BIOINFORMATICS APPLICATIONS NOTE Vol. 24 no. 17 2008, pages 19511952
 

Summary:  85. Ding,F. et al. (2008) Ab initio RNA folding by discrete molecular dynamics: from structure... /btn328 Structural bioinformatics iFoldRNA: three-dimensional RNA structure prediction and folding... ABSTRACT Summary: Three-dimensional RNA structure prediction and ...

  

Source: Dokholyan, Nikolay V. - Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill

 

Collection: Physics ; Biology and Medicine

 
48 Prospects for ab initio Protein Structural Genomics Kim T. Simons, Charlie Strauss and David Baker*
 

Summary:  Prospects for ab initio Protein Structural Genomics Kim T. Simons, Charlie Strauss and David Baker... of the ROSETTA method for ab initio protein structure prediction. Models were generated for two independently... protein. These results suggest that ab initio ...

  

Source: Baker, David - Center for Nanotechnology and NanoTechnology & Department of Biochemistry, University of Washington at Seattle

 

Collection: Chemistry ; Biotechnology

 
49 AUGUSTUS as ab initio method Mario Stanke
 

Summary:  AUGUSTUS as ab initio method Mario Stanke Institut f¨ur Mikrobiologie und Genetik Universit¨at G... ¨ottingen Germany AUGUSTUS as ab initio method ­ p.1/8 #12;Application Flow Input: DNA sequence s AUGUSTUS... algorithm This parse defines the predicted gene structure (only CDS, 1 transcript). AUGUSTUS as ...

  

Source: Foissac, Sylvain - Centre de Regulació Genòmica, Barcelona

 

Collection: Biotechnology

 
50 Estimates for the potential accuracy required in realistic protein folding simulations and structure recognition experiments
 

Summary:  must remain the global energy minimum. For an ab initio folding simulation, where the energy... required for ab initio protein folding simulations or, more modestly, for protein struc- ture recognition... accuracy required for ab ...

  

Source: Pereira de Araújo, Antônio Francisco - Departamento de Biologia Celular, University of Brasilia

 

Collection: Chemistry ; Biotechnology

 
51 Interatomic potential for silicon defects and disordered phases Joa~o F. Justo
 

Summary:  parameters in the functional form are obtained by fitting to a set of ab initio results from quantum... with ab initio and tight-binding calculations. It is the only potential known to describe both the 30... of the liquid and amorphous phases are also in good agreement with experimental and ...

  

Source: Bazant, Martin Z. - Department of Mathematics, Massachusetts Institute of Technology (MIT); Kaxiras, Efthimios - School of Engineering and Applied Sciences, Harvard University

 

Collection: Materials Science ; Mathematics ; Physics

 
52 Ab initio melting curve of copper by the phase coexistence approach L. Vocadloa)
 

Summary:  Ab initio melting curve of copper by the phase coexistence approach L. Vocadloa) Department... Street, London, WC1E 6BT, United Kingdom Received 23 October 2003; accepted 13 November 2003 Ab initio... calculations of the melting properties of copper in the pressure range 0­100 GPa are reported. The ...

  

Source: Alfè, Dario - Departments of Earth Sciences & Physics and Astronomy, University College London

 

Collection: Physics ; Geosciences

 
53 Ab initio melting curve of copper by the phase coexistence approach L. Vocadloa)
 

Summary:  Ab initio melting curve of copper by the phase coexistence approach L. Vocadloa) Department... Street, London, WC1E 6BT, United Kingdom Received 23 October 2003; accepted 13 November 2003 Ab initio... calculations of the melting properties of copper in the pressure range 0­100 GPa are reported. The ...

  

Source: Price, G. David - Department Earth Sciences, University College London; Voèadlo, Lidunka - Department Earth Sciences, University College London

 

Collection: Chemistry ; Geosciences ; Materials Science

 
54 Data Analysis of Villin Headpiece Subdomain Folding Simulations.
 

Summary:  of a given protein using computational methods. Ab initio structure prediction is the Holy Grail... shapes and has implications in drug design. Until recently ab initio structure prediction has been... Data Analysis of Villin Headpiece Subdomain Folding Simulations. Jagannath Krishnan ...

  

Source: Bejerano, Gill - Departments of Computer Science & Developmental Biology, Stanford University

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
55 Elsevier Editorial System(tm) for Journal of Nuclear Materials Manuscript Draft
 

Summary:  : Title: Ab initio-based diffusion theory and tracer diffusion in Ni-Cr and Ni-Fe alloys Article Type... Ridge, TN 37831-6376 Dear Dr. Mansur: Enclosed is a paper titled "Ab initio-based diffusion theory... -7366 (fax) Julie.dehn.tucker@gmail.com Cover Letter #12;1 Ab ...

  

Source: Wisconsin at Madison, University of - Department of Engineering Physics, Computational Materials Group

 

Collection: Fission and Nuclear Technologies ; Materials Science

 
56 1. Although it will not be possible to search the complete conformational space of a large protein (> 100a.a.) using simulation techniques for the foreseeable future,
 

Summary:  initio prediction of protein folding is probable within the next decade. 2. Given that the volume... improvements in the computational speed, force fields and algorithm design over recent years means that the ab... that the direct comparison of kinetic data on peptide folding should along with structural and ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
57 Rosetta in CASP4: Progress in Ab Initio Protein Structure Richard Bonneau,1
 

Summary:  with the clustering threshold. RESULTS FOR TARGETS FOLDED WITH THE AB INITIO PROTOCOL Overall summaries of the quality... Rosetta in CASP4: Progress in Ab Initio Protein Structure Prediction Richard Bonneau,1 Jerry Tsai,1... Laboratory, Los Alamos, New Mexico ABSTRACT Rosetta ...

  

Source: Baker, David - Center for Nanotechnology and NanoTechnology & Department of Biochemistry, University of Washington at Seattle

 

Collection: Chemistry ; Biotechnology

 
58 meeting review A brighter future for protein structure prediction
 

Summary:  of accurate align- ments, sensitive fold recognition, reason- able ab initio structure modeling and improved... using a library of known protein folds; and (iii) ab initio prediction using principles of atomic... overlap between the ab ...

  

Source: California at Davis, University of - Computer Science Department, Computer Science Theory Laboratory; Levitt, Michael - Department of Structural Biology, Stanford University

 

Collection: Biology and Medicine ; Biotechnology ; Computer Technologies and Information Sciences

 
59 Molecular simulation study of the c,,42... superlattice structure of alkanethiol self-assembled monolayers on Au,,111...
 

Summary:  structure of alkanethiols on Au 111 based on an accurate force field developed from ab initio quantum... important term in the force field. To study the Au­S interaction, Sellers et al.24 performed ab initio... clusters up to 5 Au atoms. Thus, it is desirable to perform ab ...

  

Source: Goddard III, William A. - Materials and Process Simulation Center & Department of Chemistry, California Institute of Technology

 

Collection: Materials Science

 
60 Molecular simulation study of the c,,42... superlattice structure of alkanethiol self-assembled monolayers on Au,,111...
 

Summary:  structure of alkanethiols on Au 111 based on an accurate force field developed from ab initio quantum... important term in the force field. To study the Au­S interaction, Sellers et al.24 performed ab initio... clusters up to 5 Au atoms. Thus, it is desirable to perform ab ...

  

Source: Zhang, Luzheng - Department of Chemical Engineering, University of Washington at Seattle

 

Collection: Materials Science


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61 Philosophical Magazine, Vol. 00, No. 00, DD Month 200x, 1--5
 

Summary:  yet. Based on this proposal, Nozawa and Ishii [8, 9] have computed with ab­initio methods the energies... for large supercells. Ab­initio simulations can therefore not directly be used for analysing the order... provide nearly ab­initio precision, however. We show in this paper that su#ciently accurate potentials

  

Source: Gähler, Franz - Institut für Theoretische und Angewandte Physik, Universität Stuttgart

 

Collection: Physics

 
62 Philosophical Magazine, Vol. 00, No. 00, DD Month 200x, 15
 

Summary:  yet. Based on this proposal, Nozawa and Ishii [8,9] have computed with ab-initio methods the energies... for large supercells. Ab-initio simulations can therefore not directly be used for analysing the order... provide nearly ab-initio precision, however. We show in this paper that sufficiently accurate potentials

  

Source: Gähler, Franz - Institut für Theoretische und Angewandte Physik, Universität Stuttgart

 

Collection: Physics

 
63 NATURE BIOTECHNOLOGY VOL 18 MARCH 2000 http://biotech.nature.com 283 Sequencing of the genomes of numerous organisms has forever
 

Summary:  threading. Furthermore, sev- eral ab initio folding groups have succeeded in identifying novel or near novel... folds40,41. Although additional progress in ab initio fold- ing is required (the ability to treat... than one for identifying possible ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine

 
64 PSPP: A Protein Structure Prediction Pipeline for Computing Clusters
 

Summary:  via three strategies: homology, fold recognition, and ab initio fragment assembly. In addition... sequence is routed to homology modeling, fold recogni- tion, and ab initio fragment assembly (Fig. 1... ] Rosetta Baker Ab ...

  

Source: U.S. Army Medical Research and Materiel Command's Bioinformatics Cell, Biotechnology High Performance Computing Software Applications Institute

 

Collection: Computer Technologies and Information Sciences ; Biotechnology

 
65 Curriculum Vitae of Michele Cascella, Ph.D. Present Address
 

Summary:  :19641-19646 (2006). · V. Garbuio, M. Cascella, L. Reining, R. Del Sole and O. Pulci "Ab-initio calculation... and P. Carloni "Formamide hydrolysis investigated by multiple steering ab-initio molecular dynamics"; J... position in "ab-initio molecular and materials modelling") · September 2006: First informal CMM QM

  

Source: Cuendet, Michel - Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne

 

Collection: Biology and Medicine ; Chemistry

 
66 STRUCTURE PREDICTION CASP AND OTHER COMMUNITY-WIDE
 

Summary:  replaced by the term ``fold recognition.'' ``Ab initio structure prediction'' is sometimes referred... redefined as ``new fold recogni- tion'' (Moultet al., 2005). True ab initio approaches are now limited... , such as homology modeling, fold ...

  

Source: Bourne, Philip E. - San Diego Supercomputer Center, University of California at San Diego

 

Collection: Biology and Medicine

 
67 Convergent evolution of protein structure
 

Summary:  : homology modeling, fold rec- ognition, and ab initio. Subsequently, when the 3-D structure is released... for Fold Recognition AI stands for ab initio CP stands for contacts predictions For further details see... (threading), and ab ...

  

Source: Fischer, Daniel - Center of Excellence in Bioinformatics and Life Sciences & Department of Computer Science and Engineering, State University of New York at Buffalo

 

Collection: Computer Technologies and Information Sciences ; Biotechnology ; Biology and Medicine

 
68 Halide adsorption on single-crystal silver substrates: dynamic
 

Summary:  Halide adsorption on single-crystal silver substrates: dynamic simulations and ab initio density... potential with input from ab-initio DFT slab calculations: Surface Solution Lateral potential on surface #12

  

Source: Rikvold, Per Arne - Department of Physics, Florida State University

 

Collection: Physics

 
69 Princeton Institute for Computational Science (PICSciE) Colloquium: Materials Properties from ab-initio Simulations
 

Summary:  Princeton Institute for Computational Science (PICSciE) Colloquium: Materials Properties from ab-initio... , using ab-initio, quantum simulations, in particular first principles molecular dynamics and Quantum

  

Source: Singh, Jaswinder Pal - Department of Computer Science, Princeton University

 

Collection: Computer Technologies and Information Sciences

 
70 Ab Initio Folding of Proteins Using Restraints Derived From Evolutionary Information
 

Summary:  Ab Initio Folding of Proteins Using Restraints Derived From Evolutionary Information Angel R. Ortiz... that some progress has been made on the ab initio protein folding problem. Detailed information about our... Suppl 1999;3:177­185. 1999 Wiley-Liss, Inc. Key words: ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine

 
71 Force Field Parameters for Large-Scale Computational Modeling of Sensitized TiO2 Sabas G. Abuabara
 

Summary:  for large scale computational modeling of sensitized TiO2-anatase surfaces are developed from ab initio... have been characterized at the ab initio level.30­34 While these previous quantum mechanical studies... multiple adsorbates, require large scale simulations beyond the limitations of purely ...

  

Source: Batista, Victor S.- Department of Chemistry, Yale University

 

Collection: Chemistry

 
72 On the Convergence of Protein Structure and Dynamics. Statistical Learning Studies of
 

Summary:  known as ab initio. Difficulties in this case are well known: the choice of a reduced protein repre... % identity template maps are clustered together. In 1 case ab initio generated structures are clus- tered... . The last case (chain A of PDB entry 1OJH), is an interesting exception as indeed ...

  

Source: Pollastri, Gianluca - School of Computer Science and Informatics, University College Dublin

 

Collection: Computer Technologies and Information Sciences

 
73 Vol. 42 (2011) ACTA PHYSICA POLONICA B No 34 AB INITIO NUCLEAR THEORY --PROGRESS AND
 

Summary:  Vol. 42 (2011) ACTA PHYSICA POLONICA B No 3­4 AB INITIO NUCLEAR THEORY -- PROGRESS AND PROSPECTS... of these ab initio no core methods are their flexibility for choosing (1) the Hamiltonian; (2) the method... of these approaches. #12;Ab Initio Nuclear Theory -- ...

  

Source: Magiera, Andrzej - Instytut Fizyki, Uniwersytet Jagiellonski

 

Collection: Physics

 
74 On the Convergence of Protein Structure and Dynamics. Statistical Learning Studies of
 

Summary:  known as ab initio. Difficulties in this case are well known: the choice of a reduced protein repre... identity threshold at 95% and 50% respectively, and an ab initio predicted map. For each of these maps, 200... are clustered together. In 1 case ab initio generated ...

  

Source: Passerini, Andrea - Dipartimento di Ingegneria e Scienza dell'Informazione, Università di Trento

 

Collection: Computer Technologies and Information Sciences

 
75 A MOLECULAR AND QUANTUM MECHANICAL STUDY OF INDOLE-3-ACETIC ACID
 

Summary:  , PM3) and ab initio (about fifteen DFT and RHF basis sets). Bond length matrix mxn (m = number... structure was optimized using various methods. In general, ab initio bond lengths are closer to experimental... of ab initio and also methods of the same level of ...

  

Source: Ferreira, Márcia M. C. - Instituto de Química, Universidade Estadual de Campinas

 

Collection: Chemistry

 
76 PROTINFO: secondary and tertiary protein structure Ling-Hong Hung and Ram Samudrala*
 

Summary:  ) and de novo prediction (AB). In the comparative modeling and fold recognition categories... initio folding of proteins using restraints derived from evolutionary information. Proteins, S3, 177... ­185. 10. Osguthorpe,D. (1999) Improved ab initio predictions with a ...

  

Source: Samudrala, Ram - Department of Microbiology, University of Washington at Seattle

 

Collection: Biotechnology ; Biology and Medicine

 
77 *Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1 7HX, UK;
 

Summary:  in ab initio protein folding will depend less on computer cycles and more on the design of appropriate... . This year's section on Theory and simulation begins with two reviews of ab initio protein structure... initio methods of protein structure prediction proved to ...

  

Source: Levy, Ronald M.- Department of Chemistry and Chemical Biology, Rutgers University

 

Collection: Chemistry ; Biotechnology

 
78 CSAR Focus, Edition 4, January 2000.CSAR Focus, Edition 4, January 2000.CSAR Focus, Edition 4, January 2000.CSAR Focus, Edition 4, January 2000.CSAR Focus, Edition 4, January 2000.44444 TTTTTurururururing Pring Pring Pring Pring Probes the Earobes the Ear
 

Summary:  . Parameter-free ab initio techniques based on density functional theory (DFT) have recently made enormous... unnecessary.With ab initio molecular-dynamics methods (Car- Parrinello)4 , this is true for both liquids... , January 2000.66666 Figure 2 compares our ab ...

  

Source: Alfè, Dario - Departments of Earth Sciences & Physics and Astronomy, University College London

 

Collection: Physics ; Geosciences

 
79 Nuclear Structure and Reactions (Quantum Monte Carlo, Lanczos Methods, Density Functional Methods), June 6 10
 

Summary:  and new challenges in ab initio nuclear structure and nuclear reactions" 2:00 pm Bira van Kolck "Harmonic... EFT: trapped atoms and nucleons" Tuesday, June 7 10:00 am Bruce Barrett "Ab initio shell model... systems: nuclei and the unitary Fermi gas" Thursday, June 9 10:00 am Stefano Gandolfi ...

  

Source: Washington at Seattle, University of - Department of Physics, Electroweak Interaction Research Group - Neutron Beta Decay Time Reversal Invariance Test

 

Collection: Physics

 
80 Origami with strings: predicting how proteins fold
 

Summary:  example: T0131 Ab-initio prediction: origami with strings ­ p.28/30 #12;Undertaker example: T0147 Fold... Ab initio methods Comparative modeling Results origami with strings ­ p.2/30 #12;What is Biomolecular... -recognition plus ab-initio prediction: origami with strings ­ p.29/30 ...

  

Source: Karplus, Kevin - Department of Biomolecular Engineering, University of California at Santa Cruz

 

Collection: Biotechnology ; Chemistry


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81 Physica B 378380 (2006) 898899 KOs2O6: Superconducting rattler
 

Summary:  anharmonic and broad potential well. We use ab initio energies and forces to derive the Hamiltonian... ° . Using ab initio energies and forces [8] we have constructed an effective Hamiltonian for K dynamics... . Pe and Po are polynomial radial functions obtained by fitting the ab ...

  

Source: Pickett, Warren - Department of Physics, University of California, Davis

 

Collection: Physics

 
82 Journal of the Earth Simulator, Volume 7, March 2007, 1721 First-principles Calculation on Screw Dislocation Core Properties in
 

Summary:  to deter- mine the core structure of dislocations. We use the Vienna ab initio Simulation Package [6] (VASP... of Woodward and Rao [2]. 5. Conclusion We have implemented the VASP (Vienna ab-initio simulation package) code... . Woodward, and S. I. Rao, Ab-initio simulation of iso- lated screw dislocations in ...

  

Source: Li, Ju - Department of Materials Science and Engineering, University of Pennsylvania

 

Collection: Materials Science ; Physics

 
83 All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins A. D. MacKerell, Jr.,*,, D. Bashford,, M. Bellott,, R. L. Dunbrack, Jr.,, J. D. Evanseck,,
 

Summary:  surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized... the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes... demonstrate that use of ab initio structural and ...

  

Source: Li, Yaohang - Department of Computer Science, Old Dominion University; Straub, John E. - Department of Chemistry, Boston University

 

Collection: Chemistry ; Computer Technologies and Information Sciences

 
84 Perspectives in protein-fold recognition Andrew E Torda
 

Summary:  centred on protein-fold recognition as opposed to ab initio protein-structure prediction. Fold recognition... to see which is the most appropriate for a sequence of interest. Ab initio probably means one uses any... and threading. If, however, a function will be used ...

  

Source: Kurtz, Stefan - Center for Bioinformatics, Universität Hamburg

 

Collection: Computer Technologies and Information Sciences

 
85 Project Summary and Objectives Multiscale Modeling of the Deformation of Advanced Ferritic Steels for Generation
 

Summary:  -planar cleavage of the steels, accounting for local chemistry. We also complement these ab-initio calculations... with a hybrid ab-initio/ continuum 3-D model. One particular area of emphasis will be on dislocation interaction... also complement these ab-initio calculations with traditional Molecular Dynamics (MD) simulations

  

Source: Ghoniem, Nasr M. - Department of Materials Science and Engineering, University of California at Los Angeles

 

Collection: Materials Science

 
86 1 INTRODUCTION Theories of the mineral-water interface or electrical
 

Summary:  the ab initio structures fairly accurately. These surface structures and force field parameters were used... be needed to improve upon these re- sults. 3 RESULTS 3.1 Ab initio structures and adsorption energies... , respectively) and to ab initio results (2.25 Å) ...

  

Source: South Bohemia, University of - Faculty of Science

 

Collection: Multidisciplinary Databases and Resources ; Environmental Sciences and Ecology

 
87 BioMed Central Page 1 of 16
 

Summary:  2 of 16 (page number not for citation purposes) ling, fold recognition, and ab initio prediction... identities ranging from 50% to 10% to the nearest related protein with known structure. Using our ab initio... structure is used to create the initial or seed model. In the ...

  

Source: Levitt, Michael - Department of Structural Biology, Stanford University; Samudrala, Ram - Department of Microbiology, University of Washington at Seattle

 

Collection: Biology and Medicine ; Biotechnology

 
88 Data Mining and Knowledge Discovery, 13, 110, 2006 c 2006 Springer Science + Business Media, LLC. Manufactured in the United States.
 

Summary:  boundaries. Some ab initio methods, such as tertiary structure folding approaches, average sev- eral hundred... predictions obtained from coarse ab initio simulations of protein folding to assign domain boundaries... ) and was ranked among the top ...

  

Source: Cheng, Jianlin Jack - Department of Computer Science, University of Missouri-Columbia

 

Collection: Computer Technologies and Information Sciences

 
89 3/8/2011 CAP5510 / CGS5166 1 CAP 5510: Introduction to Bioinformatics!
 

Summary:  recognition ! Threading methods ab initio methods ! From first principles ! With the help of databases #12... 2 Protein Folding! How to find minimum energy configuration? Unfolded Molten Globule State Folded... Native State Rapid (< 1s) Slow (1 ­ 1000 s) #12;3/8/2011 CAP5510 / CGS5166 3 Protein ...

  

Source: Narasimhan, Giri - School of Computer Science, Florida International University

 

Collection: Computer Technologies and Information Sciences

 
90 Ab initio protein structure prediction results using a simple distance geometry-based method
 

Summary:  to the extent that near-native fold selection is possible. Introduction Methods for ab initio protein structure... in the database. One type of ab initio method calls for the construction of a library of candidate folds, from... targets. Three of the targets were ...

  

Source: Samudrala, Ram - Department of Microbiology, University of Washington at Seattle

 

Collection: Biotechnology ; Biology and Medicine

 
91 292 Progress of Theoretical Physics Supplement No. 138, 2000 Protein Folding: Flexible Lattice Models
 

Summary:  with detailed atomic models. Preliminary applications to ab initio protein folding and distant homology... of the number) of possible protein folds have no examples in the structural databases. Thus, the ab initio... to be identified by an ab ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine

 
92 Protein structure prediction, fold recognition, homology modeling and design rely mainly on statistical effective energy
 

Summary:  successfully tested for decoy discrimination [49] and has performed reasonably well in ab initio folding tests... -molecule crystal and solvation data, as well as ab initio calculations); see MacKerell et al. [21] for a recent... state and can therefore be used as part of structure ...

  

Source: Lazaridis, Themis - Department of Chemistry, City College, City University of New York

 

Collection: Chemistry

 
93 proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Improving threading algorithms for remote
 

Summary:  from ab initio folding or built by the chunk-TASSER component of PRO-SP3 -TASSER. Results using... ­template alignments, for example, models built by (chunk-)TASSER simulations27,28 or models obtained from ab initio... such as threading or ab ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine

 
94 FoldRecognitionusingHiddenMarkov ModelsandSecondaryStructure
 

Summary:  and predicted local structure labels with ab-initio scoring scheme in undertaker. #12;... FoldRecognitionusingHiddenMarkov ModelsandSecondaryStructure KevinKarplusandRichardHughey Computer... .html UCSC Bioinformatics research and degree programs http://www.soe.ucsc.edu/research/compbio · Fold

  

Source: Karplus, Kevin - Department of Biomolecular Engineering, University of California at Santa Cruz

 

Collection: Biotechnology ; Chemistry

 
95 Protein Simulations in Confined Environments Murat Cetinkaya1
 

Summary:  , Pennsylvania State University, University Park, 16802, PA Keywords: Elastic Network Model, Ab initio... , such as elastic network model. At the atomic interaction level, we used ab initio simulations to calculate... -8 In this paper, we combined coarse-grained molecular dynamics simulations with ...

  

Source: Demirel, Melik C. - Department of Engineering Science and Mechanics, Pennsylvania State University

 

Collection: Materials Science

 
96 Treating Hydrogen Bonding in Ab Initio Calculation of Biopolymers
 

Summary:  Treating Hydrogen Bonding in Ab Initio Calculation of Biopolymers YE MEI,1 EMILIA L. WU,2 K. L. HAN... , and dipole moment are compared with those from the standard full system ab initio calculations. The result... in practical ab initio calculation of proteins. Our ...

  

Source: Zhang, John Z.H. - Department of Chemistry, New York University

 

Collection: Chemistry

 
97 Biophysical Journal Volume 85 August 2003 11451164 1145 TOUCHSTONE II: A New Approach to Ab Initio Protein
 

Summary:  ., 1991; Panchenko et al., 2000; Skolnick and Kihara, 2001); and ab initio folding (Pillardy et al., 2001... folding, where one attempts to fold a protein from a random conformation. In principle, ab initio... Biophysical Journal Volume 85 August ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine

 
98 Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma
 

Summary:  such circum- stances. Nevertheless, as this process occurs, ab initio folding will also benefit from... ) and more recently in CASP4 (13) for the difficult targets, ab initio folding methods produce better models... ), it is safe to conclude that our ...

  

Source: Kihara, Daisuke - Department of Biological Sciences, Purdue University; Lu, Hui - Department of Bioengineering, University of Illinois at Chicago; Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Biology and Medicine ; Biotechnology ; Chemistry ; Engineering

 
99 Pure Appl. Chem., Vol. 74, No. 6, pp. 907914, 2002. 2002 IUPAC
 

Summary:  of methods for predicting protein structure from sequence: compara- tive and ab initio modeling... and selecting the best match [11­13]. In the ab initio category, there is no strong dependence on database... grew more distant. Ab initio prediction Target sequences ...

  

Source: Samudrala, Ram - Department of Microbiology, University of Washington at Seattle

 

Collection: Biotechnology ; Biology and Medicine

 
100 JOURNAL DE PHYSIQUE Colloque C5, suppl6ment au nolO, Tome 49, octobre 1988
 

Summary:  JOURNAL DE PHYSIQUE Colloque C5, suppl6ment au nolO, Tome 49, octobre 1988 AB-INITIO CALCULATION... in these studies have not been entirely ab initio in the sense that assumptions regarding the starting atomic... intrinsic defects: four-memberedrings and three-fold coordinated atoms. 1. Introduction - The ...

  

Source: Ecole Polytechnique, Centre de mathématiques

 

Collection: Mathematics


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