Computational methods for macromolecules: Challenges and applications. Proceedings of the 3rd international workshop on algorithms for macromolecular modeling, New York, NY, USA, October 12--14, 2000 (Q1612912)

The articles of this volume will be reviewed individually. The preceding symposium (2nd, 1997) has been reviewed (see Zbl 0904.00046). Indexed articles: \textit{Gan, Hin Hark; Schlick, Tamar}, Methods for macromolecular modeling \((M^3)\): assessment of progress and future perspectives, 1-27 [Zbl 1138.92326] \textit{Baker, Nathan A.; Tai, Kaihsu; Henchman, Richard; Sept, David; Elcock, Adrian; Holst, Michael; McCammon, J. Andrew}, Mathematics and molecular neurobiology, 31-60 [Zbl 1138.92321] \textit{Auffinger, Pascal; Masquida, Benoit; Westhof, Eric}, Structural and dynamical characterization of nucleic acid water and ion binding sites, 61-70 [Zbl 1138.92320] \textit{Barth, Eric; Leimkuhler, Benedict; Reich, Sebastian}, A test set for molecular dynamics algorithm, 73-103 [Zbl 1138.92322] \textit{Lee, Sang-Ho; Krimm, Samuel}, Internal coordinate molecular dynamics based on the spectroscopic \(B\)-matrix, 104-128 [Zbl 1138.92331] \textit{Mann, Geoff; Yun, R. H.; Nyland, Lars; Prins, Jan; Board, John; Hermans, Jan}, The Sigma MD programm and a generic interface applicable to multi-functional programs with complex, hierarchical command structure, 129-145 [Zbl 1138.92332] \textit{Izaguirre, Jesús A.; Ma, Qun; Matthey, Thierry; Willcock, Jeremiah; Slabach, Thomas; Moore, Branden; Viamontes, George}, Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method, 146-174 [Zbl 1138.92328] \textit{Mezei, Mihaly}, On the potential of Monte Carlo methods for simulating macromolecular assemblies, 175-196 [Zbl 1138.92333] \textit{Hassan, Sergio A.; Mehler, Ernest L.; Weinstein, Harel}, Structure calculation of protein segments connecting domains with definded secondary structure: a simulated annealing Monte Carlo combined with biased scaled collective variables technique, 197-231 [Zbl 1138.92327] \textit{Fischer, Alexander; Schütte, Christof; Deuffhard, Peter; Cordes, Frank}, Hierarchical uncoupling-coupling of metastable conformations, 235-259 [Zbl 1138.92324] \textit{Galliat, T.; Deuffhard, P.; Roitzsch, R.; Cordes, F.}, Automatic identification of metastable conformations via self-organized neural networks, 260-284 [Zbl 1138.92325] \textit{Jarzynski, C.}, Equilibrium and nonequilibrium foundations of free energy computational methods, 287-303 [Zbl 1138.92329] \textit{Sugita, Yuji; Okamoto, Yuko}, Free-energy calculations in protein folding by generalized-ensemble algorithms, 304-332 [Zbl 1138.92337] \textit{Zhang, Yingkai; Liu, Haiyan; Yang, Weitao}, Ab initio QM/MM and free energy calculations of enzyme reactions, 333-355 [Zbl 1138.92341] \textit{Krasny, Robert; Duan, Zhong-Hui}, Treecode algorithms for computing nonbonded particle interactions, 359-380 [Zbl 1138.92330] \textit{Tuckerman, Mark E.; Minary, Peter; Pikahara, Katianna; Martyna, Glenn J.}, A new reciprocal space based method for treating long range interactions in ab initio and force-field based calculations for surfaces, wires and clusters, 381-410 [Zbl 1312.81138] \textit{Sandak, B.}, Efficient computational algorithms for fast electrostatics and molecular docking, 411-441 [Zbl 1153.92306] \textit{Felts, Anthony K.; Wallqvist, Anders; Gallicchio, Emilio; Bassolino, Donna; Krystek, Stanley R.; Levy, Ronald M.}, Fold recognition using the OPLS all-atom potential and the surface generalized Born solvent model, 445-476 [Zbl 1311.92146] \textit{Cammer, Stephen A.; Carter, Charles W. jun.; Tropsha, Alexander}, Identification of sequence-specific tertiary packing motifs in protein structures using Delaunay tessellation, 477-494 [Zbl 1311.92142]