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Sample search results for: ab initio protein

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1 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... Institutes of Health 2005 X "High-accuracy Protein Structure Modeling" 3 75 5 2 ab initio ab ...

  

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

 

Collection: Chemistry ; Biotechnology

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

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

  

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

 

Collection: Biotechnology ; Computer Technologies and Information Sciences

 
3 Protein Structure Analysis Iosif Vaisman
 

Summary:  Protein Structure Analysis Iosif Vaisman 2009 BINF 731 Protein Modeling Methods · Ab initio methods... · Energy-based methods · Knowledge-based methods Protein Modeling Methods · Ab initio methods: solution... Methods · ...

  

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

 

Collection: Biotechnology

 
4 AUGUSTUS as EST-, mRNA and protein-based Method
 

Summary:  ¡ and a random set of hints ¢ . P £¤ ¥ ¦¨§ © ¥ § ¥ ¥ P £¤ ¥ ¦§ © ¥ as in ab initio AUGUSTUS P... in the ab initio model. Malus effect: Gene structures with exons which are not supported by hints become... less likely than in the ab initio ...

  

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

 

Collection: Biotechnology

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

Summary:  ) (28), and the ab initio method based on neural networks (29) to predict domains for de novo proteins... , 3 five-domain proteins and 1 six-domain protein. We evaluate both template- based and ab initio... template-based and ...

  

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

 

Collection: Computer Technologies and Information Sciences

 
6 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... Probabilistic Graphical Model for Protein Structure Prediction Abstract: If we know the primary... sequence of a protein, can we predict its three dimensional structure by computational methods? This ...

  

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

 

Collection: Computer Technologies and Information Sciences

 
7 New Advance in Computational Chemistry: Full Quantum Mechanical ab Initio Computation of Streptavidin-Biotin Interaction Energy
 

Summary:  the protein molecule is decomposed into amino-acid-based fragments that are properly capped. Ab initio... between a protein and another molecule can be carried out by separate ab initio calculations... and the size of basis set used.20,28 For large ...

  

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

 

Collection: Chemistry

 
8 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

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

Summary:  An Overview of Protein Structure Prediction: From Homology to Ab Initio Final Project For Bioc218... be used to predict the protein structure from the sequence information only. Common to all Ab Initio... , most Ab Initio ...

  

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

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
10 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Ab Initio Protein Structure Prediction Using Chunk-TASSER
 

Summary:  permission. Ab Initio Protein Structure Prediction Using Chunk-TASSER Hongyi Zhou; Jeffrey Skolnick

  

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

 

Collection: Chemistry ; Biology and Medicine

 
11 Molecular fractionation with conjugate caps for full quantum mechanical calculation of proteinmolecule interaction energy
 

Summary:  mechanical ab initio interaction energy involving a macromolecule like protein is presented. In this scheme... of atoms, standard full quantum me- chanical or ab initio calculation of protein interaction energy... semiempirical methods for ...

  

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

 

Collection: Chemistry

 
12 Tara Watkins Biochem 218
 

Summary:  of the target protein is based on the structure of these previously resolved template proteins. Ab initio... for the future of ab initio protein structure prediction, although in practice many groups have effectively given... . TOUCHSTONE: an ...

  

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

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

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

Summary:  and neural networks. There are many protein disorder predictors that make use of ab initio methods... homologues for the target protein. PreDisorder14 is an ab initio protein disorder predictor designed by our... proteins. ...

  

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

 

Collection: Computer Technologies and Information Sciences

 
14 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... proteins, ab initio protein structure assembly becomes significantly more computationally expensive... / protein of a quite ...

  

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

 
15 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... as a passive dioxygen storage protein, is actually an allosteric enzyme which may control NO, CO, O2, and H2O2... substates under changes in the protein environment. #12;

  

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

 

Collection: Chemistry

 
16 March 11, 2004 22:38 WSPC/178-JTCC 00089 Journal of Theoretical and Computational Chemistry
 

Summary:  , No. 1 (2004) 43­49 c World Scientific Publishing Company FULL AB INITIO COMPUTATION OF PROTEIN... (ab initio) calculation of interaction energy involving a macromolecule like protein has recently been... a benchmark full ab ...

  

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

 

Collection: Chemistry

 
17 BMRB is a member of the wwPDB BMRB collaborates with
 

Summary:  Jobs ! Entry processing involves 4 stages " Preparation (1 job) " Ab initio (1 job per 25 structures... = prepare.log output = prepare_$(ENTRYID).out error = prepare_$(ENTRYID).err queue #12;Ab initio (From... #12;Ab initio ! Run at CHTC " Able to fall back to ...

  

Source: Liblit, Ben - Department of Computer Sciences, University of Wisconsin at Madison

 

Collection: Computer Technologies and Information Sciences

 
18 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 ...

  

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

 

Collection: Chemistry ; Biotechnology

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

Summary:  related protein in the database of solved protein structures, the PDB. Under these conditions, ab initio... . Proteins 2007;68:48­56. VVC 2007 Wiley-Liss, Inc. Key words: ab initio folding; protein folding; pro- tein... years ...

  

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

 

Collection: Chemistry ; Biology and Medicine

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

Summary:  structure must already exist. With ab initio fold- ing, we attempt to fold a protein from a random... threading algorithm for protein structure prediction that can also be applied to ab initio protein folding... simultaneously solve for ...

  

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

 

Collection: Chemistry ; Biology and Medicine


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

Summary:  Ab Initio Prediction of the Three-Dimensional Structure of a De Novo Designed Protein: A Double... University, Princeton, New Jersey ABSTRACT Ab initio structure prediction and de novo protein design are two... are presented in which a new ab ...

  

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

 

Collection: Chemistry ; Biotechnology

 
22 COMMUNICATIONS Quantum mechanical map for protein-ligand binding with application
 

Summary:  of the rigid protein and benzamidine has zero en- ergy. As shown in Fig. 2, the quantum ab initio and AMBER... /benzamidine binding complex. In this study, the full quantum mechanical ab initio energy calculation for the entire... -based fragments that are properly capped. The present MFCC ...

  

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

 

Collection: Chemistry

 
23 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... with potential template protein leads to increased exploitation. Initial search is pure exploration. The template... protein is used to guide search. If this lowers the energy, exploitation of this ...

  

Source: 

 

Collection: Engineering ; Computer Technologies and Information Sciences

 
24 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... reserved Structure All-Atom Ab Initio Folding of Proteins #12;discrete ``stripes'' in the energy landscape... -Atom Ab Initio ...

  

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

 

Collection: Chemistry ; Biology and Medicine

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

Summary:  1 1 Ab initio Protein Structure Prediction Using Pathway Models Xin Yuan, Yu Shao, and Christopher... s ab initio method, the protein conformation is represented using backbone torsion angles and fixed... . & Shao, Y. (2002). Fully automated ab ...

  

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

 

Collection: Biotechnology ; Biology and Medicine

 
26 JAMES RENNIE BEQUEST REPORT ON EXPEDITION/PROJECT/CONFERENCE
 

Summary:  a stage where ab-initio modeling has become a fact, and a reality. Structural modelling of protein-protein... available at: http://compbio.cs.toronto.edu/ B. Modelling State of Ab-initio Modeling Till now, ab-initio... that predicts protein binding sites, to learn about the new ...

  

Source: Barton, Nick - School of Biological Sciences, University of Edinburgh

 

Collection: Biology and Medicine

 
27 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

 
28 Accurate Modeling of the Intramolecular Electrostatic Energy of Proteins
 

Summary:  * level using ab initio molecular orbital theory. A collection of six electrostatic models was constructed... -were calculated from the HF/6-31G* wave functions whose energies define the ab initio energy surface... relative to ab initio energy differences between ...

  

Source: Ponder, Jay - Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis

 

Collection: Biotechnology ; Biology and Medicine

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

Summary:  that this consensus-based distance geometry method will prove useful as a tool for the ab initio prediction of protein... -native protein backbones generated by ab initio folding methods. Proteins Struct Funct GenetForthcoming. Kolinski... of ...

  

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

 
30 Use of Text Mining for Protein Structure Prediction and Functional Annotation in Lack of Sequence Homology
 

Summary:  to be developed. Ab-initio structure predic- tion and comparison is a method some of us pursued previously... used ab-initio structure prediction method. Results: We report two results: first, the literature... that uses literature to assist SCOP super-family prediction [2] significantly improves on our original ab-initio

  

Source: Rocha, Luis - School of Informatics, Indiana University

 

Collection: Computer Technologies and Information Sciences

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

Summary:  ,1998; ACCEPTEDJune I, 1998) Abstract For successful ab initio protein structure prediction, a method is needed... will prove useful as a tool for the ab initio prediction of protein structure. Materials and methods... - chain prediction upon near-native ...

  

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

 

Collection: Biotechnology ; Biology and Medicine

 
32 Protein Structure Prediction Jayanthi Sourirajan
 

Summary:  that the native state of the protein represents the global free energy minimum. Ab-initio method tries to find... -352. Bonneau R. Baker, D. (2001) Ab Initio protein structure prediction: progress and prospects. Annul. Rev... . M. and Baker D. (2001) ROSETTA in CASP4: Progress in ...

  

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

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
33 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... be modeled using ab initio methods. Our goal, after performing the modeling for all tractable proteins... to determine if they can be predicted using ...

  

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

 

Collection: Biotechnology ; Biology and Medicine

 
34 BIOCHEM218: Computational Molecular Biology Professor Douglas Brutlag
 

Summary:  Structure Prediction via Ab initio) Protein structure prediction is distinct from protein folding problem... /threading fails, one resort to predicting the structure based on physical principle alone (ab initio / protein... in predicting the ...

  

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

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
35 STRUCTURE PREDICTION CASP AND OTHER COMMUNITY-WIDE
 

Summary:  (template). If the protein has high sequence identity, homology modeling is used. Conversely, ab initio... . Approximate ab initio predictions could be made for very small proteins through exhaustive conformational... structure determination was yet to begin. More ...

  

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

 

Collection: Biology and Medicine

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

Summary:  . Proteins, S3, 186­193. 11. Samudrala,R., Xia,Y., Huang,E. and Levitt,M. (1999) Ab initio protein structure... ,R., Ruczinski,I. and Baker,D. (1999) Ab initio structure prediction of CASP3 targets using ROSETTA. Proteins, S3... . Xia,Y., Huang,E., ...

  

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

 

Collection: Biotechnology ; Biology and Medicine

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

Summary:  the procedure described above (except ab initio folding tests) not only to lattice model proteins but to also... with derived potentials Ability of the derived potential to fold model proteins is tested by their ab initio... ) poorly designed ...

  

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

 
38 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... approach is ab initio folding, where one attempts to fold a protein from a random conforma- tion.10... . TOUCHSTONE was applied to the ...

  

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

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

Summary:  quality models of protein structures produced by the thread- ing or ab initio methods described here... . & Baker, D. Ab initio structure prediction of CASP III targets using ROSETTA. Proteins Suppl. 3, 171... . Osguthorpe, D.J. Improved ab ...

  

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

 

Collection: Chemistry ; Biology and Medicine

 
40 The PDB is a Covering Set of Small Protein Structures Daisuke Kihara and Jeffrey Skolnick*
 

Summary:  models17,18 and ab initio protein structure prediction. The most successful ab initio methods incorpor... . In ab initio protein structure prediction, some authors have used structural similarity to known... ). ...

  

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


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

Summary:  , especially ab initio prediction, can be improved by segmenting the protein using the putative domain... predictions obtained from coarse ab initio simulations of protein folding to assign domain boundaries... have created DOMpro, an ab ...

  

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

 

Collection: Computer Technologies and Information Sciences

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

Summary:  Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium... ) An ab initio protein structure prediction procedure, TOUCHSTONE, was applied to all 85 small proteins... of 58 proteins ...

  

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

 
43 PSPP: A Protein Structure Prediction Pipeline for Computing Clusters
 

Summary:  structure of the protein domain must be built ab initio, i.e., the structure must be assembled using energy... ] Rosetta Baker Ab initio folder [41] [62] SCOP/ASTRAL Chothia and Murzin Database of protein folds [11] [63... the partial HTML output of an ...

  

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

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

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

  

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

 

Collection: Chemistry ; Biotechnology

 
45 Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with molecules
 

Summary:  number of atoms in proteins, the standard quantum chemistry or ab initio calculation26­28 could... not be extended to protein sys- tems. These standard ab initio methods such as Hartree­ Fock HF or density... mechanical or ab ...

  

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

 

Collection: Chemistry

 
46 Ab Initio Conformational Space Study of Model Compounds of O-Glycosides of serinediamide
 

Summary:  Ab Initio Conformational Space Study of Model Compounds of O- Glycosides of serinediamide G. I... coupled with molecular mechanics (MM2*). These rotamers were further optimized with an ab initio level... the natural preference for 1 in linkages between the carbohydrate and protein in ...

  

Source: Csonka, Gábor István - Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics

 

Collection: Materials Science ; Chemistry

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

Summary:  recently, we close this review by reminding ourselves and the reader where we are in ab initio protein... . Proteins 1999, 34:82-95. 47. Simons KT, Bonneau R, Ruczinski I, Baker D: Ab initio protein structure... potentials. ...

  

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

 

Collection: Chemistry

 
48 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... - proved to 51­54% (36­42% of 1 2). Implica- tions of a consensus method for ab initio protein structure... of the overall fold of the protein, ...

  

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

 
49 Prediction and design of macromolecular structures and interactions
 

Summary:  . This was accomplished by integrating ab initio protein structure prediction, atomic level energy refinement... ) Prediction of protein structure The picture of protein folding that motivates our approach to ab initio... (given sequence, optimize ...

  

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

 

Collection: Chemistry ; Biotechnology

 
50 Treating Hydrogen Bonding in Ab Initio Calculation of Biopolymers
 

Summary:  in practical ab initio calculation of proteins. Our result also underscores the importance of the polarization... Chem 106: 1267­1276, 2006 Key words: ab initio; protein; hydrogen bonding; -helix; -sheet; polarization... Treating Hydrogen Bonding in ...

  

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

 

Collection: Chemistry

 
51 MEETING REPORT Modeling of Protein Interactions in Genomes
 

Summary:  modeling, threading, or ab initio methods of protein structures being determined by X-ray crystallography... MEETING REPORT Modeling of Protein Interactions in Genomes Sandor Vajda,*,1 Ilya A. Vakser,2... INTRODUCTION Protein interactions play pivotal roles in various aspects of the ...

  

Source: Vajda, Sandor - Department of Biomedical Engineering, Boston University

 

Collection: Biotechnology ; Biology and Medicine

 
52 Convergent evolution of protein structure
 

Summary:  protein has no significant sequence similar- ity to a known structure. Ab initio. Since our structural... (threading), and ab initio. In what follows we describe each of these approaches very briefly (we refer... , then the chess program would jump to the 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

 
53 G53BIO Coursework PART 1: Survey Report
 

Summary:  · Homology modelling · Fold recognition · Ab-Initio modelling · Steps of PSP · Template identification... for G53BIO will focus on the bioinformatics of proteins. The outcome should be a 5000 words report... deadline: August 31st , 2011 at 16:00 Protein Structure and Protein Structure Prediction ...

  

Source: Bacardit, Jaume - School of Computer Science, University of Nottingham

 

Collection: Computer Technologies and Information Sciences

 
54 Predicting Interresidue Contacts Using Templates and Pathways
 

Summary:  and ab initio methods were combined to produce accurate, protein-like contact maps. Pathways sometimes... parts of the protein pack together, we can improve the accuracy of the ab initio method... scoring functions. J Mol Biol 1997;268:209­225. 20. Bystroff C, Shao ...

  

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

 

Collection: Biotechnology ; Biology and Medicine

 
55 Nearly Deterministic Methods for Optimising Protein Geometry Gundolf Schenk, Andrew Torda
 

Summary:  self consistency within this framework. State of the art Methods for ab initio protein structure... Nearly Deterministic Methods for Optimising Protein Geometry Gundolf Schenk, Andrew Torda ZBH... @zbh.uni-hamburg.de Aim We are interested in ·self consistent mean field methods and ·the ...

  

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

 

Collection: Computer Technologies and Information Sciences

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

Summary:  1 Title of article: Scoring functions for ab initio protein structure prediction Suggested running... of the small proteins that serve as ab initio targets. This implies that if one tries to fold a small protein... head: Scoring functions for ...

  

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

 

Collection: Biotechnology ; Biology and Medicine

 
57 The continuity of protein structure space is an intrinsic property of proteins
 

Summary:  in the ab initio limit. Proteins 68:48­56. 34. Andreeva A, et al. (2008) Data growth and its impact... by TASSER in the ab initio limit (33). A number of interesting results were found. Using the original... /turns experience a conformational bias and can dissolve and reform simulation. ...

  

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

 

Collection: Chemistry ; Biology and Medicine

 
58 292 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

 
59 BSC 4934: QBIC Capstone Workshop" Giri Narasimhan
 

Summary:  on fold recognition " Threading methods ab initio methods " From first principles " With the help... @cs.fiu.edu http://www.cs.fiu.edu/~giri/teach/BSC4934_Su10.html July 2010 #12;7/21/10 Protein Structures... ;7/21/10 Proteins" Primary structure is the sequence of amino acid residues of the ...

  

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

 

Collection: Computer Technologies and Information Sciences

 
60 BioMed Central Page 1 of 16
 

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


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61 986 nature structural biology structural genomics supplement november 2000 Evolution has produced families of pro-
 

Summary:  of the modeled protein. So far, the ab initio methods have produced models with the cor- rect fold for only a few... small protein domains. Nevertheless, recent progress in ab initio prediction raises hope that structural... recourse are the ab ...

  

Source: Sali, Andrej - Department of Biochemistry and Biophysics, University of California at San Francisco

 

Collection: Biology and Medicine ; Biotechnology

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

Summary:  Rosetta in CASP4: Progress in Ab Initio Protein Structure Prediction Richard Bonneau,1 Jerry Tsai,1... Laboratory, Los Alamos, New Mexico ABSTRACT Rosetta ab initio protein structure predictions in CASP4 were... D. Ab initio ...

  

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

 

Collection: Chemistry ; Biotechnology

 
63 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... client and its use in folding NTL9, the slowest-folding protein ever simulated ab initio with fidelity... distributed computing platform, the Folding@home project has ...

  

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

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
64 Analysis of Methods for Predicting Protein Fold and Remote Homologue Recognition
 

Summary:  - 352. Bonneau, R.; Baker, D. Ab Initio Protein Structure Prediction: Progress and Prospects. Annu. Rev... (Baker, et al., 2001). The first approach, ab initio methods, predicts the structure from sequence alone... structures (Bonneau, et al, 2001). The ab ...

  

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

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
65 Prof. Dr. P. Entel --Theoretische Tieftemperaturphysik Projekt: MolekulardynamikSimulation mikroskopisch heterogener Systeme
 

Summary:  , wobei Struktur und Dynamik der vorgeschlagenen Systeme mit Hilfe von ab initio und Standard... gezeigt sind. F˜ur diesen Prim˜arkomplex bestehend aus Chromophor und Aminos˜auren sollen ab initio... durchgef˜uhrt worden, wenn auch mit leicht unterschiedlichen Ergebnissen [4--7]. Ab ...

  

Source: Duisburg-Essen, Universität - Fachbereich Physik, Theoretical Low-Temperature Physics Group

 

Collection: Physics

 
66 Prof. Dr. P. Entel Theoretische Tieftemperaturphysik Projekt: Molekulardynamik-Simulation mikroskopisch heterogener Systeme
 

Summary:  unterschiedlichen Ergebnissen [4­7]. Ab initio Simulationen der Wechselwirkung von Retinal und Protein sind bisher... , wobei Struktur und Dynamik der vorgeschlagenen Systeme mit Hilfe von ab initio und Standard... ¨ur diesen Prim¨arkomplex bestehend aus Chromophor und Aminos¨auren ...

  

Source: Duisburg-Essen, Universität - Fachbereich Physik, Theoretical Low-Temperature Physics Group

 

Collection: Physics

 
67 Fully Quantum Mechanical Energy Optimization for ProteinLigand Structure
 

Summary:  mechanical ab initio protein­ligand interaction energy and its gradients that are used in energy minimization... , it is desirable to employ ab initio quantum mechanical cal- culation for geometry optimization of the protein... full ab ...

  

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

 

Collection: Chemistry

 
68 Gnomon NCBI eukaryotic gene prediction A. Souvorov , Y. Kapustin, B. Kiryutin, V. Chetvernin,
 

Summary:  of homology searching with ab initio modeling. The use of ab initio is threefold: a) we use ab initio scores... a partial alignment we extend this alignment using the ab initio prediction, and c) when... there is no ...

  

Source: Levin, Judith G. - Laboratory of Molecular Genetics, National Institutes of Health

 

Collection: Biology and Medicine

 
69 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch http://genomebiology.com/2002/3/2/reports/4004.1
 

Summary:  . The unified method has the potential to predict active sites from ab initio models of protein structure, using... that combines in one the three most used methods - homol- ogy modeling, threading and ab initio prediction... , Piscataway, USA) then pre- sented his laboratory's recent ...

  

Source: Gerstein, Mark - Department of Molecular Biophysics and Biochemistry, Yale University; Zhang, ZhaoLei - Banting and Best Department of Medical Research, University of Toronto

 

Collection: Biology and Medicine ; Biotechnology

 
70 Nearly Deterministic Methods for Optimising Protein Geometry Gundolf Schenk, Andrew Torda
 

Summary:  self consistency within this framework. State of the art Methods for ab initio protein structure... Nearly Deterministic Methods for Optimising Protein Geometry Gundolf Schenk, Andrew Torda ZBH... @zbh.uni-hamburg.de Aim We are interested in ·self consistent mean field methods and ·the ...

  

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

 

Collection: Computer Technologies and Information Sciences

 
71 216 Current Protein and Peptide Science, 2009, 10, 216-228 1389-2037/09 $55.00+.00 2009 Bentham Science Publishers Ltd.
 

Summary:  , and ab initio methods. The homology modeling method is based on the observation that proteins... follows. The last cate- gory, ab initio or de novo prediction methods, essentially fold a protein model... -based statistical potentials, mimicking a physical ...

  

Source: Kihara, Daisuke - Department of Biological Sciences, Purdue University

 

Collection: Biology and Medicine ; Biotechnology

 
72 http://genomebiology.com/2000/1/3/reports/4014.1 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch
 

Summary:  proteins identified by the human genome. On the subject of ab initio protein structure prediction, David... initio protein structure prediction methods (including Bakers) still give structures in the four to eight... conference, held in Elsinore, Denmark, 27-30 ...

  

Source: Ussery, David W. - Center for Biological Sequence Analysis, Institute of Biotechnology, Danmarks Tekniske Universitet

 

Collection: Biotechnology

 
73 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

 
74 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

 
75 FOR THE RECORD Decoys `R' Us: A database of incorrect conformations
 

Summary:  Y, Huang E, Levitt M. 1999. Ab initio protein structure prediction using a combined hierarchical... that if a method that can sample the conformational space in an ab initio manner to produce the distribution... be tested exhaustively. Data sets generated in an ab ...

  

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

 

Collection: Biology and Medicine ; Biotechnology

 
76 Application of Sparse NMR Restraints to Large-Scale Protein Structure Prediction
 

Summary:  ; Skolnick et al., 2000), but the application of pure ab initio approaches to protein structures has been... , it has been found that in ab initio protein structure prediction, sparse distance restraints can... types of proteins in PDB amenable for ...

  

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

 

Collection: Chemistry ; Biology and Medicine

 
77 The Dependence of All-Atom Statistical Potentials on Structural Training Database
 

Summary:  . A combined approach for ab initio construction of low resolution protein tertiary structures from sequence... ;Xia, Y., E. S. Huang, M. Levitt, and R. Samudrala. 2000. Ab initio construction of protein tertiary... a significant dependence. The construction of two ...

  

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

 

Collection: Biology and Medicine

 
78 498 Current Protein and Peptide Science, 2010, 11, 498-514 1389-2037/10 $55.00+.00 2010 Bentham Science Publishers Ltd.
 

Summary:  to systematically improve protein modeling based on the laws of physics [46]. The ab initio methods utilize first... with the protein sequence and secondary structure information. The ab initio prediction of 3D Struc- ture... of small globu- lar ...

  

Source: Jayaram, Bhyravabotla - Supercomputing Facility for Bioinformatics and Computational Biology Project & School of Biological Sciences, Indian Institute of Technology, Delhi

 

Collection: Biology and Medicine

 
79 Iosif Vaisman Email: ivaisman@gmu.edu
 

Summary:  Methods · Ab initio methods: solution of a protein folding problem search in conformational space · Energy... Families families All alpha proteins 179 299 480 All beta proteins 126 248 462 Alpha and beta proteins (a/b... ) 121 199 542 Alpha and ...

  

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

 

Collection: Biotechnology

 
80 BioMed Central Page 1 of 10
 

Summary:  Research article Ab initio modeling of small proteins by iterative TASSER simulations Sitao Wu1, Jeffrey Skolnick2... -resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA... -9], and (iii) ...

  

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

 

Collection: Chemistry ; Biology and Medicine


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81 Progress in Biophysics & Molecular Biology 73 (2000) 339345 Structural proteomics: prospects for high throughput
 

Summary:  } just being erroneous results of ab initio gene-prediction methods. Surprisingly, a retrospective... is nowhere near complete. For example, in the worm, C. elegans, less than half of the predicted proteins have... will be to ``finish the job'', that is, to ascribe a function to each of the proteins that ...

  

Source: Gerstein, Mark - Department of Molecular Biophysics and Biochemistry, Yale University

 

Collection: Biology and Medicine ; Biotechnology

 
82 Poster session Retinal protein action
 

Summary:  (Duisburg) Ab initio calculations on retinal model chromophores Minoru Sugihara, Volker Buß, Peter Entel... Waheed A. Adeagbo, Peter Entel (Duisburg) Melting of water clusters from ab initio point of view Heike C... /Cr/Fe trilayers with extended transition metal impurities: An ab ...

  

Source: Duisburg-Essen, Universität - Fachbereich Physik, Theoretical Low-Temperature Physics Group

 

Collection: Physics

 
83 Efforts toward Developing Direct Probes of Protein Dynamics Matthew E. Cremeens, Hiroshi Fujisaki, Yong Zhang, Jorg Zimmermann, Laura B. Sagle,
 

Summary:  of ab initio calculations (Supporting Information), we assign the low frequency absorption... and Figure 1). On the basis of ab initio calculations, we assign the two lower frequency absorptions... an ab initio surface (B3LYP/6-31+G(d,p)) to model vibrational ...

  

Source: Straub, John E. - Department of Chemistry, Boston University

 

Collection: Chemistry

 
84 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

 
85 A Web-Accessible Protein Structure Prediction Pipeline Michael S. Lee
 

Summary:  protein. The computationally-intensive ab initio component benefits greatly from the use of multiple... prediction: comparative (homology) modeling, fold recognition, and ab initio fragment assembly. The pipeline... by sequence alignment or by the PROSPECTII threading procedure, then a ...

  

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

 
86 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

 
87 Protein Structure Prediction by Comparative Modeling: An Analysis of Methodology
 

Summary:  to advance more quickly. Two main approaches to computational structure determination exist: ab initio... prediction and comparative modeling. Ab initio or de novo prediction uses physical and chemical first... conformations.4 Consequently, loop prediction algorithms must often employ ab ...

  

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

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
88 Automatic prediction of protein function B. Rosta,b,c,
 

Summary:  the way for ab initio prediction of protein function. Key words: Genome analysis; protein function... ]. Ab initio methods predict localisation for all proteins at lower accuracy Another approach... is problematic and limited in scope. Therefore, ...

  

Source: Rost, Burkhard - Department of Biochemistry and Molecular Biophysics, Columbia University

 

Collection: Biology and Medicine

 
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 Folding! ...

  

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

 

Collection: Computer Technologies and Information Sciences

 
90 Proceedings of International Joint Conference on Neural Networks, Montreal, Canada, July 31 -August 4, 2005 Prediction of Contact Map Integrated PNN with
 

Summary:  . Biol. 2000; 296: 1319-1331. [31 Simons, K. T., Strauss, C. & Baker, D. Prospects for ab initio protein... . An ab initio protein structure prediction method that uses threading-based tertiary restraints Proc... ], inverse folding or threading method [2] and ...

  

Source: Hefei Institute of Intelligent Machines - Intelligent Computing Lab

 

Collection: Computer Technologies and Information Sciences

 
91 Dr. Ivano Tavernelli Laboratory of Computational Chemistry and Biochemistry
 

Summary:  Publications 1) Tapavicza E., Tavernelli I., Rothlisberger U., "Ab initio Molecular Dynamics with Quantum... ., "Ab initio molecular dynamics for molecules with variable numbers of electrons", Phys. Rev. Lett., 88... , 213002 (2002). F. Most Recent Invited Talks (2007-2008) 1) SimBioMa workshop on ...

  

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

 

Collection: Biology and Medicine ; Chemistry

 
92 Intrinsically Disordered Proteins A Tutorial Jianhan Chen1
 

Summary:  of protein targets. Hybrid methods choose either template-based or ab initio method to make prediction... into five categories [8], including ab initio methods [9-28], clustering methods [29-31], template... -based methods are often used with ab ...

  

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

 

Collection: Computer Technologies and Information Sciences

 
93 Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model
 

Summary:  Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First... a methodology based primarily on ab initio quantum chemistry, and a first generation polarizable protein force... diminshes Force Field for Proteins ...

  

Source: Berne, Bruce J. - Department of Chemistry, Columbia University

 

Collection: Physics ; Chemistry

 
94 PHYSICS COLLOQUIUM, partially funded by the GSFEI David Baker
 

Summary:  will describe: (1) Significant progress in ab initio computation of the structures of small proteins from... for a number of small proteins (Bradley et al, Science 2005; boinc... .bakerlab.org/rosetta/top_predictions.html). (2) The high accuracy prediction of structures of protein-protein ...

  

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

 

Collection: Physics

 
95 www.sciencemag.org SCIENCE VOL 311 24 MARCH 2006 1709 LETTERS I BOOKS I POLICY FORUM I EDUCATION FORUM I PERSPECTIVES
 

Summary:  RNAs because they often include ab initio predicted exons (1). Our strategy was to construct... expression pat- terns of ab initio predicted exons (2), we argue that this does not prove the physical... are unlikely to have been in the training sets of ab initio exon ...

  

Source: Frey, Brendan J. - Department of Electrical and Computer Engineering, University of Toronto

 

Collection: Computer Technologies and Information Sciences

 
96 Ab Initio Construction of Protein Tertiary Structures Using a Hierarchical Approach
 

Summary:  Ab Initio Construction of Protein Tertiary Structures Using a Hierarchical Approach Yu Xia1 , Enoch... under the auspices of the CASP3 experiment, where we did ab initio structure predictions for 12 proteins... search space (Levinthal, 1968). Novel methods have ...

  

Source: Huang, Enoch S. - Bioinformatics Program, Boston University; Levitt, Michael - Department of Structural Biology, Stanford University; Samudrala, Ram - Department of Microbiology, University of Washington at Seattle; Xia, Yu "Brandon" - Bioinformatics Program and Department of Chemistry, Boston University

 

Collection: Biology and Medicine ; Biotechnology

 
97 proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Improving threading algorithms for remote
 

Summary:  structures in CASP6. Proteins 2005;61(Suppl. 7):91­98. 28. Zhou H, Skolnick J. Ab initio protein structure... for ab initio protein structural genomics. J Mol Biol 2001;306:1191­1199. 30. Zhou H, Skolnick J. Protein... ...

  

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

 

Collection: Chemistry ; Biology and Medicine

 
98 BLASTing Tools BLAST & FASTA: Search database for
 

Summary:  on fold recognition ­ Threading methods · ab initio methods ­ From first principles ­ With the help... alignment · Prosite, Interpro, Pfam: Search query sequence for patterns representative of protein families 2... 13) #12;PSI-BLAST · Version of BLAST to find protein families for a given query ...

  

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

 

Collection: Computer Technologies and Information Sciences

 
99 The Yeast Resource Center Public Data Repository Michael Riffle, Lars Malmstrom and Trisha N. Davis*
 

Summary:  structures are predicted for protein domains, as parsed from the Ginzu algorithm (5). Ab initio structure pre... ,C., Strauss,C.E. and Baker,D. (2001) Rosetta in CASP4: progress in ab initio protein structure prediction... ,D. (1999) Ab ...

  

Source: Davis, Trisha N. - Department of Biochemistry, University of Washington at Seattle

 

Collection: Biology and Medicine ; Environmental Management and Restoration Technologies

 
100 The Cation-Interaction Stabilizing Interaction Between a
 

Summary:  Electrostatic Model sp2 carbon is more electronegative than hydrogen ab initio calculated electrostatic... the ab initio energy results (~OPLS) ·Apply new energy model to 593 nonhomologous, high- resolution... - Interactions in Structural Biology ? Most statistical analyses of protein ...

  

Source: Stoltz, Brian M. - Division of Chemistry and Chemical Engineering, California Institute of Technology

 

Collection: Chemistry


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