FPGA acceleration of rigid molecule interactions

We show how an application of central importance to computational biochemistry can be implemented efficiently on an FPGA. This requires reformulating the algorithm and taking advantage of application characteristics to maximize device utilization.

[1]  Martin C. Herbordt,et al.  Rigid Molecule Docking: FPGA Reconfiguration for Alternative Force Laws , 2006, EURASIP J. Adv. Signal Process..

[2]  M. Sternberg,et al.  Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.

[3]  J. Mccammon,et al.  Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. , 1999, Journal of structural biology.

[4]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[5]  Z. Weng,et al.  A novel shape complementarity scoring function for protein‐protein docking , 2003, Proteins.

[6]  Martin C. Herbordt,et al.  FPGA Acceleration of Rigid Molecule Interactions , 2004, FPL.

[7]  Yuan-Ping Pang,et al.  EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases , 2001, J. Comput. Chem..

[8]  D. Ritchie,et al.  Protein docking using spherical polar Fourier correlations , 2000, Proteins.

[9]  Earl E. Swartzlander,et al.  Systolic Signal Processing Systems , 1987 .

[10]  Sandor Vajda,et al.  ClusPro: an automated docking and discrimination method for the prediction of protein complexes , 2004, Bioinform..

[11]  William H. Press,et al.  Numerical recipes in C. The art of scientific computing , 1987 .

[12]  William H. Press,et al.  The Art of Scientific Computing Second Edition , 1998 .

[13]  Anil K. Jain,et al.  Convolution on Splash 2 , 1995, Proceedings IEEE Symposium on FPGAs for Custom Computing Machines.

[14]  H. T. Kung.  Why systolic architectures? , 1982, Computer.

[15]  Z. Weng,et al.  ZDOCK: An initial‐stage protein‐docking algorithm , 2003, Proteins.

[16]  Stephen R. Comeau,et al.  PIPER: An FFT‐based protein docking program with pairwise potentials , 2006, Proteins.

[17]  William H. Press,et al.  Book-Review - Numerical Recipes in Pascal - the Art of Scientific Computing , 1989 .

[18]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[19]  E. Katchalski‐Katzir,et al.  Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Zhiping Weng,et al.  Docking unbound proteins using shape complementarity, desolvation, and electrostatics , 2002, Proteins.