Completion and refinement of 3‐D homology models with restricted molecular dynamics: Application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis
暂无分享,去创建一个
G Vriend | J A Flohil | H J C Berendsen | G. Vriend | J.A. Flohil | H. Berendsen | Gerrit Vriend | J. A. Flohil
[1] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[2] M C Peitsch,et al. ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. , 1996, Biochemical Society transactions.
[3] G Vriend,et al. WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.
[4] Wilfred F. van Gunsteren,et al. GROMOS Force Field , 2002 .
[5] D. Case,et al. Modification of the Generalized Born Model Suitable for Macromolecules , 2000 .
[6] C. Brooks,et al. Comparative Study of the Folding Free Energy Landscape of a Three-Stranded β-Sheet Protein with Explicit and Implicit Solvent Models , 2000 .
[7] D. Baker,et al. 2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15. , 2001, Journal of the American Chemical Society.
[8] R. Abagyan,et al. Recognition of distantly related proteins through energy calculations , 1994, Proteins.
[9] Herman J. C. Berendsen,et al. A Molecular Dynamics Study of the Decane/Water Interface , 1993 .
[10] Evelyn Camon,et al. The EMBL Nucleotide Sequence Database , 2004, Nucleic acids research.
[11] C. Sander,et al. Errors in protein structures , 1996, Nature.
[12] R Sánchez,et al. Evaluation of comparative protein structure modeling by MODELLER‐3 , 1997, Proteins.
[13] W. Pearson. Rapid and sensitive sequence comparison with FASTP and FASTA. , 1990, Methods in enzymology.
[14] K Fidelis,et al. A large‐scale experiment to assess protein structure prediction methods , 1995, Proteins.
[15] R A Friesner,et al. Prediction of loop geometries using a generalized born model of solvation effects , 1999, Proteins.
[16] J. Ponder,et al. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.
[17] A. Lesk,et al. The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.
[18] R Abagyan,et al. Homology modeling by the ICM method , 1995, Proteins.
[19] X. Daura,et al. Parametrization of aliphatic CHn united atoms of GROMOS96 force field , 1998 .
[20] Roland L. Dunbrack,et al. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. , 1993, Journal of molecular biology.
[21] C. Sander,et al. Quality control of protein models : directional atomic contact analysis , 1993 .
[22] D. Baker,et al. 2.1 and 1.8 Å Average Cα RMSD Structure Predictions on Two Small Proteins, HP-36 and S15 , 2001 .
[23] M Levitt,et al. Recognizing native folds by the arrangement of hydrophobic and polar residues. , 1995, Journal of molecular biology.
[24] G T Montelione,et al. Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: Application in predicting the three‐dimensional structure of murine homeodomain Msx‐1 , 1997, Protein science : a publication of the Protein Society.
[25] C Sander,et al. The use of position‐specific rotamers in model building by homology , 1995, Proteins.
[26] S H Bryant,et al. A retrospective analysis of CASP2 threading predictions , 1997, Proteins.
[27] T. Alwyn Jones,et al. CASP3 comparative modeling evaluation , 1999, Proteins.
[28] C. Sander,et al. Fast and simple monte carlo algorithm for side chain optimization in proteins: Application to model building by homology , 1992, Proteins.
[29] Alan E. Mark,et al. The GROMOS96 Manual and User Guide , 1996 .
[30] Berk Hess,et al. LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..
[31] J Moult,et al. The current state of the art in protein structure prediction. , 1996, Current opinion in biotechnology.
[32] C. Sander,et al. Database of homology‐derived protein structures and the structural meaning of sequence alignment , 1991, Proteins.
[33] T. Hubbard,et al. Critical assessment of methods of protein structure prediction (CASP): Round III , 1999, Proteins.
[34] D. van der Spoel,et al. GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .
[35] Berk Hess,et al. Improving Efficiency of Large Time-Scale Molecular Dynamics Simulations of Hydrogen-Rich Systems , 1999 .
[36] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[37] Chris Sander,et al. Objectively judging the quality of a protein structure from a Ramachandran plot , 1997, Comput. Appl. Biosci..
[38] B. Rost. Twilight zone of protein sequence alignments. , 1999, Protein engineering.
[39] H. Berendsen,et al. Interaction Models for Water in Relation to Protein Hydration , 1981 .
[40] Michael Levitt,et al. A brighter future for protein structure prediction , 1999, Nature Structural Biology.