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  • 1
    Electronic Resource
    Electronic Resource
    Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 29-37 
    Details
    ISSN: 0887-3585
    Keywords: deformation zones ; prediction map building ; homology modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Five models by homology containing insertions and deletions and ranging from 33% to 48% sequence identity to the known homologue, and one high sequence identity (85%) model were built for the CASP2 meeting. For all five low identity targets: (i) our starting models were improved by the Internal Coordinate Mechanics (ICM) energy optimization, (ii) the refined models were consistently better than those built with the automatic SWISS-MODEL program, and (iii) the refined models differed by less than 2% from the best model submitted, as judged by the residue contact area difference (CAD) measure [Abagyan, R.A., Totrov, M.J. Mol. Biol. 268:678-685, 1997]. The CAD measure is proposed for ranking models built by homology instead of global root-mean-square deviation, which is frequently dominated by insignificant yet large contributions from incorrectly predicted fragments or side chains. We demonstrate that the precise identification of regions of local backbone deviation is an independent and crucial step in the homology modeling procedure after alignment, since aligned fragments can strongly deviate from the template at various distances from the alignment gap or even in the ungapped parts of the alignment. We show that a local alignment score can be used as an indicator of such local deviation. While four short loops of the meeting targets were predicted by database search, the best loop 1 from target T0028, for which the correct database fragment was not found, was predicted by Internal Coordinate Mechanics global energy optimization at 1.2 Å accuracy. A classification scheme for errors in homology modeling is proposed. Proteins, Suppl. 1:29-37, 1997.© 1998 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Recognition of distantly related proteins through energy calculations (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 132-140 
    Details
    ISSN: 0887-3585
    Keywords: distant protein folds ; sequence homology ; database searching ; profile analysis ; protein structure comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new method to detect remote relationships between protein sequences and known three-dimensional structures based on direct energy calculations and without reliance on statistics has been developed. The likelihood of a residue to occupy a given position on the structural template was represented by an estimate of the stabilization free energy made after explicit prediction of the substituted side chain conformation. The profile matrix derived from these energy values and modified by increasing the residue self-exchange values successfully predicted compatibility of heatshock protein and globin sequences with the three-dimensional structures of actin and phycocyanin, respectively, from a full protein sequence databank search. The high sensitivity of the method makes it a unique tool for predicting the three-dimensional fold for the rapidly growing number of protein sequences. © 1994 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190206
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  • 3
    Electronic Resource
    Electronic Resource
    A new method for modeling large-scale rearrangements of protein domains (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 410-424 
    Details
    ISSN: 0887-3585
    Keywords: domain movements ; inter-domain linkers ; conformational calculations ; Monte Carlo-minimization method ; Bence-Jones protein ; lysine/arginine/ornithine-binding protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method for modeling large-scale rearrangements of protein domains connected by a single- or a double-stranded linker is proposed. Multidomain proteins may undergo substantial domain displacements, while their intradomain structure remains essentially unchanged. The method allows automatic identification of an interdomain linker and builds an all-atom model of a protein structure in internal coordinates. Torsion angles belonging to the interdomain linkers and side chains potentially able to form domain interfaces are set free while all remaining torsions, bond lengths, and bond angles are fixed. Large-scale sampling of the reduced torsion conformational subspace is effected with the “biased probability Monte Carlo-minimization” method [Abagyan, R.A., Totrov, M.M. (1994): J. Mol. Biol. 235, 983-1002]. Solvation and side-chain entropic contributions are added to the energy function. A special procedure has been developed to generate concerted deformations of a double-stranded interdomain linker in such a way that the polypeptide chain continuity is preserved. The method was tested on Bence-Jones protein with a single-stranded linker and lysine/arginine/ornithine-binding (LAO) protein with a double-stranded linker. For each protein, structurally diverse low-energy conformations with ideal covalent geometry were generated, and an overlap between two sets of conformations generated starting from the crystallographically determined “closed” and “open” forms was found. One of the low-energy conformations generated in a run starting from the LAO “closed” form was only 2.2 Å away from the structure of the “open” form. The method can be useful in predicting the scope of possible domain rearrangements of a multidomain protein. Proteins 27:410-424, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Flexible protein-ligand docking by global energy optimization in internal coordinates (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 215-220 
    Details
    ISSN: 0887-3585
    Keywords: molecular recognition ; ligand binding ; flexible docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Eight protein-ligand complexes were simulated by using global optimization of a complex energy function, including solvation, surface tension, and side-chain entropy in the internal coordinate space of the flexible ligand and the receptor side chains [Abagyan, R.A., Totrov, M.M. J. Mol. Biol. 235:983-1002, 1994]. The procedure uses two types of efficient random moves, a pseudobrownian positional move [Abagyan, R.A., Totrov, M.M., Kuznetsov, D.A. J. Comp. Chem. 15:488-506, 1994] and a Biased-Probability multitorsion move [Abagyan, R.A., Totrov, M.M. J. Mol. Biol. 235:983-1002, 1994], each accompanied by full local energy minimization. The best docking solutions were further ranked according to the interaction energy, which included intramolecular deformation energies of both receptor and ligand, the interaction energy, surface tension, side-chain entropic contribution, and an electrostatic term evaluated as a boundary element solution of the Poisson equation with the molecular surface as a dielectric boundary. The geometrical accuracy of the docking solutions ranged from 30% to 70% according to the relative displacement error measure at a 1.5 Å scale. Similar results were obtained when the explicit receptor atoms were replaced with a grid potential. Proteins, Suppl. 1:215-220, 1997. © 1998 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Homology modeling by the ICM method (1995)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995), S. 403-414 
    Details
    ISSN: 0887-3585
    Keywords: modeling by homology ; protein structure prediction ; loop modeling ; side-chain placement ; Monte Carlo procedure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Five models have been built by the ICM method for the Comparative Modeling section of the Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. The targets have homologous proteins with known three-dimensional structure with sequence identity ranging from 25 to 77%. After alignment of the target sequence with the related three-dimensional structure, the modeling procedure consists of two subproblems: side-chain prediction and loop prediction. The ICM method approaches these problems with the following steps: (1) a starting model is created based on the homologous structure with the conserved portion fixed and the noncon-served portion having standard covalent geometry and free torsion angles; (2) the Biased Probability Monte Carlo (BPMC) procedure is applied to search the subspaces of either all the nonconservative side-chain torsion angles or torsion angles in a loop backbone and surrounding side chains. A special algorithm was designed to generate low-energy loop deformations. The BPMC procedure globally optimizes the energy function consisting of ECEPP/3 and solvation energy terms. Comparison of the predictions with the NMR or crystallographic solutions reveals a high proportion of correctly predicted side chains. The loops were not correctly predicted because imprinted distortions of the backbone increased the energy of the near-native conformation and thus made the solution unrecognizable. Interestingly, the energy terms were found to be reliable and the sampling of conformational space sufficient. The implications of this finding for the strategies of future comparative modeling are discussed. © 1995 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340230314
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