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Original Articles

New Methodology for Computer-Aided Modelling of Biomolecular Structure and Dynamics 2. Local Deformations and Cycles

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Pages 833-845 | Received 25 Jul 1988, Published online: 21 May 2012

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Solène Grosdidier, Max Totrov & Juan Fernández-Recio. (2009) Computer applications for prediction of protein–protein interactions and rational drug design. Advances and Applications in Bioinformatics and Chemistry 2, pages 101-123.
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VladimirE. Dorofeyev & AlexeyK. Mazur. (1993) Investigation of Conformational Equilibrium of Polypeptides by Internal Coordinate Stochastic Dynamics. Met5 -Enkephalin. Journal of Biomolecular Structure and Dynamics 11:1, pages 143-167.
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AlexeyK. Mazur & RubenA. Abagyan. (1989) New Methodology for Computer-Aided Modelling of Biomolecular Structure and Dynamics 1. Non-Cyclic Structures. Journal of Biomolecular Structure and Dynamics 6:4, pages 815-832.
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Mahsa Bayati, Miriam Leeser & Jaydeep P. Bardhan. (2020) High‐performance transformation of protein structure representation from internal to Cartesian coordinates. Journal of Computational Chemistry 41:24, pages 2104-2114.
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Nicholas K. Bodmer & James J. Havranek. (2018) Efficient minimization of multipole electrostatic potentials in torsion space. PLOS ONE 13:4, pages e0195578.
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Maciej Blaszczyk, Dominik Gront, Sebastian Kmiecik, Katarzyna Ziolkowska, Marta Panek & Andrzej Kolinski. 2014. Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes 25 53 .
Vamshi K. Gangupomu, Jeffrey R. Wagner, In-Hee Park, Abhinandan Jain & Nagarajan Vaidehi. (2013) Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations. Biophysical Journal 104:9, pages 1999-2008.
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William III, Donald Brenner, Sergey Lyshevski & Gerald IafrateAndres Jaramillo-Botero, Jamil Tahir-Kheli, Paul von Allmen & William III. 2012. Handbook of Nanoscience, Engineering, and Technology, Third Edition. Handbook of Nanoscience, Engineering, and Technology, Third Edition 935 982 .
Christoph Grebner, Johannes Becker, Svetlana Stepanenko & Bernd Engels. (2011) Efficiency of tabu-search-based conformational search algorithms. Journal of Computational Chemistry 32:10, pages 2245-2253.
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Andres Jaramillo-Botero, Robert Nielsen, Ravi Abrol, Julius Su, Tod Pascal, Jonathan Mueller & William A. GoddardIIIIII. 2012. Multiscale Molecular Methods in Applied Chemistry. Multiscale Molecular Methods in Applied Chemistry 1 42 .
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Svetlana Stepanenko & Bernd Engels. (2009) Tabu Search Based Strategies for Conformational Search. The Journal of Physical Chemistry A 113:43, pages 11699-11705.
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Rudranarayan M. Mukherjee, Paul S. Crozier, Steven J. Plimpton & Kurt S. Anderson. (2008) Substructured molecular dynamics using multibody dynamics algorithms. International Journal of Non-Linear Mechanics 43:10, pages 1040-1055.
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Chu Wang, Philip Bradley & David Baker. (2007) Protein–Protein Docking with Backbone Flexibility. Journal of Molecular Biology 373:2, pages 503-519.
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Sang-Ho Lee, Kim Palmo & Samuel Krimm. (2007) A comparative study of molecular dynamics in Cartesian and in internal coordinates: Dynamical instability in the latter caused by nonlinearity of the equations of motion. Journal of Computational Chemistry 28:6, pages 1107-1118.
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Pablo Echenique & Iván Calvo. (2006) Explicit factorization of external coordinates in constrained statistical mechanics models. Journal of Computational Chemistry 27:14, pages 1748-1755.
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Pablo Echenique & J. L. Alonso. (2006) Definition of Systematic, Approximately Separable, and Modular Internal Coordinates (SASMIC) for macromolecular simulation. Journal of Computational Chemistry 27:10, pages 1076-1087.
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Andrew J. Bordner & Ruben Abagyan. (2006) Ab initio prediction of peptide‐MHC binding geometry for diverse class I MHC allotypes. Proteins: Structure, Function, and Bioinformatics 63:3, pages 512-526.
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Benjamin Bardiaux, Thérèse E. Malliavin, Michael Nilges & Alexey K. Mazur. (2006) Comparison of Different Torsion Angle Approaches for NMR Structure Determination. Journal of Biomolecular NMR 34:3, pages 153-166.
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Olayiwola A. Adekoya, Ronny Helland, Nils-Peder Willassen & Ingebrigt Sylte. (2005) Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family. Proteins: Structure, Function, and Bioinformatics 62:2, pages 435-449.
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Vsevolod Katritch, Maxim Totrov & Ruben Abagyan. (2003) ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field. Journal of Computational Chemistry 24:2, pages 254-265.
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Juan Fernández-Recio, Maxim Totrov & Ruben Abagyan. (2009) Soft protein-protein docking in internal coordinates. Protein Science 11:2, pages 280-291.
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Christopher Bystroff. (2001) An alternative derivation of the equations of motion in torsion space for a branched linear chain. Protein Engineering, Design and Selection 14:11, pages 825-828.
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Alexey Mazur. 2001. Computational Biochemistry and Biophysics. Computational Biochemistry and Biophysics.
Alexey K. Mazur. (1999) Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion. The Journal of Chemical Physics 111:4, pages 1407-1414.
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William J. Wedemeyer & Harold A. Scheraga. (1999) Exact analytical loop closure in proteins using polynomial equations. Journal of Computational Chemistry 20:8, pages 819-844.
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Ruben A Abagyan & Maxim Totrov. (1999) Ab InitioFolding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure. Journal of Computational Physics 151:1, pages 402-421.
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Michael Petukhov, David Cregut, Cláaaudio M. Soares & Luis Serrano. (2008) Local water bridges and protein conformational stability. Protein Science 8:10, pages 1982-1989.
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Vladimir Maiorov & Ruben Abagyan. (1998) Energy strain in three-dimensional protein structures. Folding and Design 3:4, pages 259-269.
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F. Sartori, B. Melchers, H. Böttcher & E. W. Knapp. (1998) An energy function for dynamics simulations of polypeptides in torsion angle space. The Journal of Chemical Physics 108:19, pages 8264-8276.
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WING HUNG WONG, YAN CUI & RUN SHENG CHEN. (1998) Torsional Relaxation for Biopolymers. Journal of Computational Biology 5:4, pages 655-665.
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Siqian He & Harold A. Scheraga. (1998) Macromolecular conformational dynamics in torsional angle space. The Journal of Chemical Physics 108:1, pages 271-286.
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Tamar Schlick, Eric Barth & Margaret Mandziuk. (1997) BIOMOLECULAR DYNAMICS AT LONG TIMESTEPS:Bridging the Timescale Gap Between Simulation and Experimentation. Annual Review of Biophysics and Biomolecular Structure 26:1, pages 181-222.
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Vladimir Maiorov & Ruben Abagyan. (1997) A new method for modeling large-scale rearrangements of protein domains. Proteins: Structure, Function, and Genetics 27:3, pages 410-424.
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James Turner, Paul K. Weiner, Barry Robson, Ravi Venugopal, Harry SchubeleIIIIII & Ramen Singh. 1997. Computer Simulation of Biomolecular Systems. Computer Simulation of Biomolecular Systems 122 149 .
Ruben A. Abagyan. 1997. Computer Simulation of Biomolecular Systems. Computer Simulation of Biomolecular Systems 363 394 .
Ruben Abagyan, Serge Batalov, Timothy Cardozo, Maxim Totrov, Jeremy Webber & Yingyao Zhou. (1997) Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search. Proteins: Structure, Function, and Genetics 29:S1, pages 29-37.
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James Turner, Paul Weiner, Barry Robson, Ravi Venugopal, Harry SchubeleIIIIII & Ramen Singh. (2004) Reduced variable molecular dynamics. Journal of Computational Chemistry 16:10, pages 1271-1290.
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Timothy F. Havel & Igor Najfeld. (1995) Applications of geometric algebra to the theory of molecular conformation 2. The local deformation problem. Journal of Molecular Structure: THEOCHEM 336:2-3, pages 175-189.
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Patrick Argos & Ruben Abagyan. (1994) The protein folding problem: Finding a few minimums in a near infinite space. Computers & Chemistry 18:3, pages 225-231.
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Ruben Abagyan, Maxim Totrov & Dmitry Kuznetsov. (2004) ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. Journal of Computational Chemistry 15:5, pages 488-506.
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Frank Eisenhaber & Patrick Argos. (2004) Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency. Journal of Computational Chemistry 14:11, pages 1272-1280.
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Axel T. Brünger & Michael Nilges. (2009) Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMRspectroscopy. Quarterly Reviews of Biophysics 26:1, pages 49-125.
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R.A. Abagyan, F. Eisenmenger & P. Argos. 1993. Computer Aided Innovation of New Materials II. Computer Aided Innovation of New Materials II 1241 1246 .
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Kathleen A. Palmer & Harold A. Scheraga. (1991) Standard-geometry chains fitted to X-ray derived structures: Validation of the rigid-geometry approximation. I. Chain closure through a limited search of ?loop? conformations. Journal of Computational Chemistry 12:4, pages 505-526.
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A.K Mazur, V.E Dorofeev & R.A Abagyan. (1991) Derivation and testing of explicit equations of motion for polymers described by internal coordinates. Journal of Computational Physics 92:2, pages 261-272.
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Kenneth D. Gibson & Harold A. Scheraga. (1990) Variable step molecular dynamics: An exploratory technique for peptides with fixed geometry. Journal of Computational Chemistry 11:4, pages 468-486.
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