Reviews in Computational Chemistry

Author Index

381

Scho¨ n, J., 204 Schrader, D. M., 199

Schreiber, G., 92, 93, 95, 96 Schreiner, P. R., 94 Schroeder, M., 251

Schuettler, H.-B., 341, 342, 343, 344 Schug, J. C., 296

Schulten, K. S., 342

Schults, D. W., 264 Schulz, H., 277

Schulze-Kremer, S., 277, 278 Schutte, C. J. H., 294 Schwabl, F., 302

Schwarz, H., 197 Schwarz, W. H. E., 197 Schweins, T., 56 Schweizer, M., 202 Scott, N. S., 318

Scott, P. R., 306, 308, 309 Searle, M. S., 54

Searles, D., 314

Searls, D. B., 286 Seasholtz, M. B., 289 Sebald, W., 93 Sedlacek, B., 290 Seefeldi, M., 334, 344 Seeger, R., 200

Seel, M., 320 Seelig, F. F., 297 Segal, G. A., 307 Seger, G., 204 Seibel, G. L., 58, 50

Seijo, L., 197, 198, 202, 203 Sekar, K., 47

Sellers, H. L., 283 Selzer, T., 93 Semenov, S. G., 308 Semenov, V. A., 263

Seminario, J. M., 201, 315, 318, 331, 344 Sen, K., 284

Sensen, C., 95

Sergeev, N. M., 304, 306 Serov, V. V., 291 Sewell, W., 272 Seybold, P. G., 253, 254 Seydel, J. K., 346

Shaik, S., 198, 315 Shakhnovich, E. I., 55 Shamir, R., 94 Shanzer, A., 346 Shapiro, B. A., 270 Sharaf, M. A., 287 Shariv, I., 95

Sharp, K. A., 56, 59

Shasha, D., 270

Shavitt, I., 201, 202, 264

Shaw, K., 264

Shchembelov, G. A., 308

Shchipin, Y. K., 262

Sheikhet, I. I., 312, 315

Shekhter, V. M., 300

Sheldrick, G. M., 291

Sheleg, A. U., 290

Shen, B. J., 93

Shenkin, P. S., 57

Sheridan, R. P., 47, 49

Sherman, C. J., 51

Shi, J., 250

Shimanouchi, T., 46, 97

Shimizu, K., 302

Shimizu, T., 280

Shindyalov, I. N., 46, 97

Shinohara, S., 301

Shirokov, A. M., 321

Shishibori, T., 268, 269

Shlifer, G., 252

Shluger, A. L., 314

Shoemaker, D. P., 289

Shoichet, B. K., 48, 49, 56, 95, 96

Shortley, G. H., 196

Shorygin, P. P., 313

Showalter, K., 251, 253

Shreider, Yu. A., 336

Shuker, S. B., 46

Shusterman, A. J., 283, 284, 334

Shvarov, Yu. V., 265

Siani, M. A., 58

Sibanda, B. L., 46

Siddiqui, K. J., 289

Siegbahn, P. E. M., 200, 202

Siepmann, J. I., 344

Signorini, J., 251

Silipo, C., 348

Silis, Ya. Ya., 264

Silva Fernandes, F. M. S., 270, 286, 319

Silver, B. L., 199

Silverman, B. D., 339

Silverman, R. B., 350

Silvi, B., 333

Simkin, B. Ya., 312, 315

Simmons, R. M. A., 48

Simon, J. C., 262

Simon, Z., 305, 345, 346

Simonov, V. D., 263, 275

Simons, J., 303

Simons, S., 295

382	Author Index
Simonson, T., 96, 334, 344		Srolovitz, D. J., 339
Sinanoglu, O., 304		Stahl, M., 47, 48, 58, 59
Singh, S., 47, 59, 284, 343		Stanley, H. E., 252, 268
Singh, U. C., 50		States, D. J., 53, 56, 95
Sippl, M. J., 57		Statz, H., 198
Sjøvoll, M., 200, 202		Steele, D., 293
Skaane, H., 199		Steer, R. P., 203
Skeats, M. G., 251		Stegmann, R., 197
Skillman, A. G., 53		Stehle, P., 294
Sklar, L., 253		Steinfeld, J. I., 250
Skolnick, J., 57, 92		Steinmetzer, T., 53
Skolnik, F., 333		Stepanek, V., 273
Slater, J. C., 294, 306, 307		Stern, O., 195
Smalas, A. O., 94		Sternberg, M. J. E., 46, 56, 92, 93, 94, 95,
Smellie, A. S., 52		96
Smeyers, Y. G., 282, 318, 319,		Stevenson, D., 266
330		Still, W. C., 57
Smit, B., 253, 342		Stillinger, F. H., 251, 307
Smith, D. A., 283		Stirtan, W. G., 59
Smith, D. E., 263		Stocken, L. A., 317
Smith, D. W., 277, 305		Stoica, L., 262
Smith, H., 301		Stoll, H., 198
Smith, J., 340		Stolz, H., 320
Smith, J. C., 97		Stoneham, A. M., 332
Smith, N. O., 337		Storey, S. H., 290
Smith, R., 343		Stote, R., 97
Smith, R. B., 272		Stouch, T. R., 55
Smith, V. H., 311, 312		Stouten, P. F. W., 53, 57, 59
Smith, W. B., 333		Stover, B. J., 336
Smythe, M. L., 55, 59		Straatsma, T. P., 51, 93
Snel, W. L. B., 92		Stratula, C., 263
Snijders, J. G., 199, 201		Straub, J., 97
Snyder, J. P., 46		Strauss, H. L., 295
Snyder, L. R., 267		Streitwieser, A., Jr., 294, 304, 306
Sobolev, V., 52		Stroud, D. G., 344
Sobolev, V. V., 321		Strynadka, N. C., 96
Sokalski, W. A., 270		Stuper, A. J., 264
Solov’ev, V. V., 274		Stuper, E., 264
Solov’eva, L. P., 290		Sturrock, C. P., 278
Soltzberg, L. J., 262, 266		Subbiah, S., 46
Sommerer, S. O., 197		Sudavtsova, V. S., 263
Sonntag, R. E., 340		Sudbeck, E. A., 47
Sorescu, G., 263		Sudo, Y., 265
Speed, T., 278		Suhai, S., 277, 279
Spellmeyer, D. C., 58, 95		Sumners, D., 342
Spiegelman, C., 288		Sun, E., 58
Spiegelmann, F., 197		Sun, Y., 49, 53
Spiess, H. W., 322		Sunakawa, S., 301
Spratley, R. D., 295		Sundaralingam, M., 47
Springborg, M., 322		Sundelof, J. G., 59
Squires, G. L., 302		Sundius, T. R., 337
Sree Harsha, K. S., 266		Surjan, P. R., 303, 312
Srinivasan, M., 92		Sussman, F., 56

	Author Index	383
Sussman, J. L., 341	Ter Haar, D., 298, 336
Sutcliffe, B. T., 304, 306, 307	Terent’ev, P. B., 272
Suter, U. W., 341, 351	Terpstra, D., 264
Sutton, A. P., 321	Testa, B., 251, 252, 253, 254, 350
Suyama, A., 267	Teukolsky, S. A., 95, 202
Suzuki, I., 267, 279	Thakkar, A. J., 262
Suzuki, M., 321	Theodorou, D. N., 334
Suzumura, T., 201	Theophanides, T., 343
Swaminathan, S., 53, 56, 95	Thierry, J. C., 292
Swanson, C. A., 53, 56	Thoma, J. U., 352
Sweetnam, P. M., 59	Thomas, J. M., 332
Swift, M. L., 270	Thomas, P. D., 57
Sygusch, J., 56	Thomasson, K. A., 94
Sykes, R. A., 53, 59	Thompson, D. L., 344
Szabo, A., 299, 300, 301, 340	Thompson, M. A., 318
Szasz, L., 311	Thompson, M. J., 92
Szondy, T., 304	Thompson, R. L., 339
	Thompson, W. J., 54
Tachikawa, H., 302	Thompson, W. T., 281
Tadeusiewicz, R., 263	Thorn, K. S., 96
Taft, R., 263	Thornton, J. M., 46, 55, 57, 92
Tainer, J. A., 53, 56	Threlkeld, P. G., 48
Takada, K., 299	Tichy, M., 346
Takagi, T., 278, 279	Tildesley, D. J., 250, 339, 340
Takahashi, H., 333	Titov, A. V., 198
Takao, Y., 280	Toffoli, T., 251
Takasugi, M., 275	Tokita, S., 300, 312, 347
Tame, J. R. H., 47	Tokizane, S., 276
Tanabe, K., 347	Tokuyama, M., 344
Tanabe, T., 321	Tomasi, J., 315
Tanaka, H., 251, 313	Tominaga, N., 312
Tanaka, M., 269, 339, 348	Tomioka, N., 49, 56
Tang, Y. Q., 55	Tomoda, S., 347
Tao, H., 56	Toney, J. H., 59
Tarroni, R., 200	Torda, A. E., 52
Tasumi, M., 46, 97, 279	Torres, M., 272
Tatchen, J., 198, 202, 204	Tosi, C., 268
Tatevskii, V. M., 305	Toth, J., 292
Tatewski, W. M., 295	Totrov, M., 52, 94, 95, 96
Taylor, I. C. A., 59	Toulhoat, H., 333
Taylor, J. B., 347, 348	Touloukian, Y. S., 271
Taylor, J. M., 204	Town, W. G., 271
Taylor, J. R., 204	Trabka, J., 263
Taylor, M. R., 292	Tramontano, A., 46
Taylor, P., 56, 319	Trickey, S. B., 307, 313
Taylor, P. L., 319	Trifonov, E. D., 295
Taylor, P. R., 200, 314	Trinajstic, N., 266, 352, 353
Taylor, W. R., 57	Trivedi, H. P., 198
Teichteil, C. H., 197, 198, 203	Trohalaki, S., 351
Teitelboim, C., 312, 314	Trosset, J. Y., 52
Tello, D., 92	Truhlar, D. G., 280, 281, 283, 319, 322, 337,
Temkin, O. N., 353	344, 351
Ten Eyk, L. F., 95	Trushin, Yu. V., 291

384	Author Index
Tschinke, V., 60		Van Lenthe, J. H., 322
Tsipis, C. A., 316		van Os, N. M., 253
Ts’o, P. O. P., 325, 327		Van Rijsbergen, C. J., 273
Tsukerblat, B. S., 314		Van Santen, R. A., 344
Tsuzuki, T., 302		Van Wylen, G. J., 340
Tucker, T. J., 54		Van Zeggeren, F., 290
Tung, R. D., 48		Varney, M. D., 56
Turbovich, M. L., 268		Vashishta, P., 351
Turchi, P. E. A., 322		Vasmatzis, V., 54
Tute, M., 253		Vassos, B. H., 269
Tute, M. S., 346		Vecchi, M. P., 51
Tyurina, L. A., 275		Veda, A., 342
		Vedani, A., 46
Uchida, N., 314		Veerapandian, P., 350
Udenfriend, S., 346		Veillard, A., 306, 312
Ueda, A., 340		Vejby-Christiansen, L., 253
Ueda, Y., 311		Veldkamp, A., 197
Uemura, M., 275		Velichko, T. I., 292
Uetz, P., 92		Venita, H., 270
Ugi, I. K., 268, 269		Venkataraghavan, R., 49
Uhlenbeck, G., 196		Venkatesan, K., 291, 298
Ukhov, V. F., 280, 337		Vereecken, L., 250
Ulam, S. M., 251		Vergoten, V., 343
Ulhaq, S., 59		Verkhivker, G. M., 51,
Ullmann, G. M., 94		55
Ulstrups, J., 338		Vernoslov, S. E., 268
Underwood, D. J., 47, 49		Veselov, M. G., 312, 321
Urban, M., 308		Veszpremi, T., 303
Uryu, N., 300		Vetokhin, V. N., 261
Ustynyuk, Yu. A., 308		Vetterling, W. T., 95, 202
		Veyts, I. V., 292
Vacca, J. P., 54		Vida, J. A., 346
Vahtras, O., 201, 203		Vieth, M., 57
Vaiman, G. E., 310		Vignale, G., 318
Vajda, S., 48, 57, 94, 96		Vijayadamodar, G., 92
Vakser, I. A., 94, 95		Vikic-Topic, D., 270, 353
Valk, H., 296		Vilgis, T. A., 341
Vallet, V., 203		Villafranca, J. E., 55
van Aalten, D. M. F., 96		Villar, H. O., 283, 284
Vanag, V. K., 254		Villaverde, M. C., 56
Van Camp, P. E., 320, 321		Vinter, J. G., 349
Vandeginste, B. G. M., 287, 289		Vishniac, G. Y., 251
Vanderwall, D. E., 59		Visscher, L., 199, 201
van de Waterbeemd, H., 252, 349,		Visser, O., 199, 201
350		Viswanadhan, V. N., 56
Van Doren, V. E., 320		Vitek, V., 339
van Galen, P. J. M., 56		Vittoria, A., 348
van Geerestein, V. J., 58		Vladimir, M. I., 313
van Gunsteren, W. F., 52, 54, 337, 339, 341,		Vleduts, G. E., 271
343		Vogl, O., 333
Van Koningsveld, H., 290		Volkenstein, M. V., 336
Van Leeuwen, P. W. N. M., 322		Volkov, A. I., 267
van Lenthe, E., 201		Volkov, S. V., 320

Author Index

385

Volkov, V. B., 307

Von Blanckenhagen, P., 339 von der Saal, W., 58

von Itzstein, M., 59 von Keitz, S., 276 von Keitz, W., 276

von Nagy-Felsobuki, E., 314 von Neumann, J., 251 Vorob’ev, S. A., 265

Vose, C., 59 Vriend, G., 52, 96 Vriens, G. N., 253

Vyboishchikov, S. F., 197

Wada, A., 267

Wade, R. C., 47, 52, 93, 94, 95

Wadt, W. R., 197

Wagniere, G. H., 306

Wahl, A. C., 263

Wahlgren, U., 198, 199, 200

Wai, J. M., 54

Wako, H., 276

Walecka, J. D., 296

Waletzke, M., 202, 204

Walgraef, D., 341

Walker, T. E. H., 199, 305, 306

Walkinshaw, M. D., 56

Waller, C. L., 55

Wallqvist, A., 52, 55, 92

Walls, P. H., 56

Walrafen, G. E., 252

Walsh, D. A., 47

Walter, A., 253

Walter, J., 293

Walters, D. E., 348

Walters, W. P., 47, 48, 58, 59

Walz, A., 272

Wampler, J. E., 95

Wang, J., 52

Wang, D., 311

Wang, J. H., 275

Wang, J. T. L., 270

Wang, R. X., 55

Wang, S., 55, 60

Wang, S. M., 56

Wang, Y., 93

Want, D., 264

Ward, S. A., 273

Warnatz, J., 338, 342

Warr, W. A., 274, 275, 276

Warshel, A., 54, 56, 282, 285

Washio, T., 53

Waskell, L., 95

Wasserman, S., 275

Wasserman, Z. R., 53

Waszkowycz, B., 53, 59

Watanabe, M., 97

Watenpaugh, K. D., 293

Waterman, M., 94

Waterman, M. S., 278, 284

Waters, D. C., 48

Watson, D. G., 50

Watson, R. E., 197

Watson, S., 59

Waugh, J. L. T., 319

Weber, E., 332

Weber, H. W., 252

Weber, J., 350

Weber, L., 53

Webster, B., 301

Wefing, S., 49

Wegiel, N., 264

Weidman, D. P., 334

Weiner, P. K., 50, 339, 341, 343

Weiner, S. J., 50

Weinstein, H., 309

Weinstein, J. N., 56

Weissberger, A., 261

Weissbluth, M., 199

Weissig, H., 46, 97

Welch, W., 47

Wells, J. A., 92

Weltner, W., Jr., 199

Weng, Z., 57, 93, 94

Wengelin, F., 261

Wentzel, G., 204

Wermuth, C. G., 348

Werner, H.-J., 198, 200, 202

Wesson, L., 94

Westbrook, J., 46, 97

Westhead, D. R., 52, 53, 57

Wever, J., 314

Whalen, J. W., 340

Whangbo, M. H., 300

Wheeler, R. G., 198

White, C. L., 59

White, H. F., 59

Whitlock, P. A., 338

Whitten, D. H., 307

Wiberg, K. B., 304

Wiggins, G., 276

Wiggins, M., 54

Wigner, E. P., 199, 296

Wilcox, G. L., 281

Wilde, R. E., 343

Wildman, S. A., 198

386 Author Index

Wilhelmi, B., 266

Wilkins, C. L., 262, 293

Wilkinson, A. J., 341, 343

Willett, P., 47, 50, 56, 269, 274, 276, 350, 351

Williams, A. R., 319

Williams, D. H., 54

Williams, G. J. B., 46, 97

Williams, M. E., 272, 273

Williams, P., 265

Willis, H. A., 292

Willson, R. C., 93

Wilson, E. B., Jr., 293

Wilson, P., 94

Wilson, R. J., 352

Wilson, S., 266, 270, 281, 282, 303, 312, 314,

317, 318, 330

Wilson, T., 276

Wimmer, E., 351

Winter, G., 346

Winter, N. W., 198

Wiorkiewicz-Kuczera, J., 97

Wipff, G., 283

Wipke, W. T., 56, 263, 271

Wiscount, C. M., 54

Wlodawer, A., 56

Wolf, H. C., 302

Wolfram, S., 251

Wolfson, H. J., 49, 50, 94, 95

Wolfson, H. L., 94

Wolman, Y., 274

Woltersdorf, O. W., 54

Wong, A. K., 58

Woods, J. M., 59

Woolley, R. G., 309

Woolridge, K. R. H., 346

Wooten, J. K., 199

Wouthuysen, S. A., 196

Wrobel, G., 267

Wu, D., 299

Wu, J. K., 59

Wu, T. Y., 300

Wu, W., 59

Wu, X.-G., 254

Wylie, W., 59

Xavier, K. A., 93

Xu, D., 93

Xu, G., 300, 311

Xu, K., 59

Yabushita, S., 202

Yamabe, S., 313, 314, 347

Yamaguchi, I., 312

Yamaguchi, K., 267, 269, 313, 347

Yamaguchi, Y., 315

Yamamoto, R., 339

Yamamoto, S., 321

Yamamoto, Y., 266, 331

Yanagida, H., 274

Yang, M., 92

Yang, W., 313

Yarkony, D. R., 196, 200, 201, 203, 316

Yasukawa, T., 278

Yatsimirskii, K. B., 352

Yatsuyanagi, Y., 302

Yazaki, Y., 280

Yeates, T. O., 92

Yin, D., 97

Yip, S., 333

Yonezawa, F., 341

Yonezawa, T., 261, 299, 300

Yoshida, M., 267, 269, 274

Yoshida, S., 315, 316

Yoshimine, M., 202

Yoshimura, T., 265, 267, 269, 277, 287

Young, S. C., 53

Young, S. D., 54

Young, S. S., 60

Yu, X., 277

Yue, S., 51

Yusipov, M. M., 264

Zahradnik, R., 297, 298, 299, 305

Zaikov, G. E., 318

Zaitsev, I. D., 264

Zanelli, J., 314

Zannetti, P., 270

Zannini, Z., 335

Zare, R. N., 199

Zasukha, V. A., 320

Zbinden, P., 46

Zefirov, N. S., 353

Zeigarnik, A. V., 353

Zeiger, E., 278

Zeleny, W. B., 297

Zeller, W. J., 349

Zenkevich, I. G., 268

Zepp, G., 297

Zerner, M. C., 308, 310, 313, 314, 316, 319,

326, 327, 328, 329, 330, 331

Zhang, C., 54

Zhang, J. Z. H., 345

Zhang, Z., 202

Zharskii, I. M., 267

Author Index

387

Zhdanov, Yu. A., 273

Zhidomirov, G. M., 308

Zhogolev, D. A., 307

Zhu, P., 310

Zhu, Y., 310

Zhukov, V. P., 306

Ziegler, E., 262, 265

Ziegler, T., 316

Zielinski, T. J., 270

Ziessow, D., 290

Zimmerman, F., 96

Zimmerman, H. E., 306

Ziock, K., 295

Zivkovic, T. P., 268, 270

Zoller, M., 281, 331

Zou, X. Q., 49

Zozulya, A. F., 264

Zuelicke, L., 296, 300

Zugay, J. A., 54

Zupan, J., 288, 289, 291, 351

Zuse, K., 251

Zwanziger, H. W., 289

Subject Index

Computer programs are denoted in boldface; databases and journals are in italics.

A*-algorithm, 20 Absolute gravity, 218, 219

Absorption, distribution, metabolism, and excretion/elimination (ADME), 38, 221

Accelrys, viii

Accessible surface area, 25 Acid dissociation, 234

ADAM, 7

AMBER, 26

AMBER force field, 14, 15, 18, 19, 81 American Chemical Society (ACS), v, 255 Amphiphile, 231

Anchor fragments, 12, 14

Angular momentum, 100, 102, 103, 109, 121

Angular momentum operator, 111, 112, 144, 151, 157

Anharmonicity, 170

Anomalous Zeeman effect, 103, 105 Antibodies, 62

Antimalaria agents, 39 Antisymmetric operator, 111 Antisymmetry, 111 Antitumor agent, 38 Aqueous diffusion, 228 Aqueous solution, 205

Artificial intelligence books, 286 Associated rate constants, 206 Association rates of proteins, 63, 75 Asynchronous movement, 213 Atomic hydrophobicity constants, 26

Atomic solvation parameters (ASP), 28, 70, 71, 81

Atoms, 172

Aufbau principle, 108

AutoDOCK, 2, 16 Automated docking, 41, 43

Automated protein-protein docking, 69 Automation, 61

Available Chemicals Directory (ACD), 30, 38, 39

Avoided crossing, 177, 178

Backbone flexibility, 81, 85, 87, 88 Backtracking, 14

Barnase, 63, 64, 65, 66, 82, 83, 84, 89 Barstar, 63, 64, 65, 66, 82, 89

Base fragments, 12 Basis set expansion, 191 Basis states, 101 Bayesian regression, 29

Belousov-Zhabotinsky oscillating reaction, 242 Benchmark docking, 91

Bezier splines, 18 Biased distortions, 81

Binding affinity, 2, 3, 11, 23, 24, 29, 33, 34, 38, 42, 62, 63

Binding conformations, 67

Binding free energies, 3, 23, 26, 27, 30 Binding mode, 2, 25, 40, 44, 82 Binding site, 2, 5, 31, 36, 44 Bioinformatics, v, 61

Biological screening, 37 Biotechnology, 62 Biotin, 30, 39

Bit string, 14

BLEEP function, 32, 33 Blind prediction, 41

BNSOC, 169 Bohr-Sommerfeld theory, 121 Boiling point, 223 Boltzmann distribution, 179 Books, 255, 322, 356

Born equation, 27

389

390 Subject Index

Born-Oppenheimer effects, 161

Boson irreducible representations, 140, 158 Bound-bound interactions, 188 Bound-continuum interactions, 189

Bound electronic states, 187 Boundary cell, 210

Bra-ket notation, 128 Branch & bound, 20 Breaking parameters, 226

Breaking probability, 216, 223 Breaking rules, 216

Breit-Pauli spin-orbit Hamiltonian, 125, 193 Breit-Pauli spin-orbit integrals, 161 Breit-Pauli spin-spin coupling operator, 147 Breit-Pauli theory, 182

Brownian dynamics, 75, 84

BUILDER, 23 Bulk solvent, 81

Buried surfaces, 31, 34, 78

CAChe, ix

Calmodulin, 79

Cambridge Structural Database (CSD), 14, 39

CAMLab, 19

CAplus, vi, 256 Carbon monoxide, 189

Cartesian coordinates, 18 Cartesian Gaussians, 161 Cartesian space, 17

Cartesian triplet spin functions, 180 Cathepsin D, 23

Cell, 209

Cell membrane, 232 Cell movement, 212 Cell shape, 210

Cellular automata, xi, 205, 207, 208 CH radical, 175

Character table, 141, 142 Charge complementarity, 65

CHARMM, 27, 64 CHARMm force field, 19 CHARMM force field, 82

Chemical Abstracts Service (CAS), v, 256 Chemical complementary scores, 25 Chemical information books, 259, 271 Chemical matching, 25

Chemical properties, 205 Chemical reactions, 205 Chemical scores, 24, 25 Cheminformatics, v Chemometrics books, 287

ChemScore, 34

Chromatographic separation, 216, 247

Chromosome, 15

CIPSO, 170

Clebsch-Gordan (CG) coefficient, 149 Clique-detection algorithm, 7 Clique-search, 6, 18

CLIX, 7

Cluster, 9 Clustering, 10, 22

Cocrystallized ligands, 30, 41

COLUMBUS, 169

CombiDOCK, 22

Combinatorial chemistry, 21, 37, 40 Combinatorial docking, 22 Combinatorial libraries, 21 Combinatorial optimization, 3, 16, 81 Commutation relations, 113, 115 Compatibility, 6

Complete enumeration, 75 Complete-linkage hierarchical clustering, 10 Complexity, 221

Compound acquisition, 37 Compound tensor operators, 145

Computational chemistry, 255, 260, 280 Computational docking studies, 67 Computer-aided ligand design, x Computer-aided molecular design books, 345 Computers in chemistry books, 261 Concoord method, 83

CONCORD, 36 Configuration, 220

Configuration interaction (CI), 127, 149, 160, 163

Configuration state functions (CSFs), 166 Conformational change, 24, 83 Conformational ensemble, 11, 83 Conformational entropy, 29 Conformational flexibility, 70, 82 Conformational search techniques, 79 Conformational space, 2, 11, 74 Conformations, 13, 14, 18, 19, 21 Consensus scoring, x, 4, 33, 44 Conserved binding site, 42

Contact scores, 24 Containment potentials, 27 Continuum wave functions, 189 Contracted basis sets, 162 Cooling schedule, 16

Copper atom, 173 Core molecule, 22

Core-electron integrals, 129 Core-valence integrals, 129

CORINA, 14, 36 Correlation energies, 169

Subject Index

391

Correspondence principle, 121 Coulomb integral, 129, 131, 161 Coupled-cluster electronic structure, 166 Coupled differential rate equations, 206 Coupling procedures, 167

Critical Assessment of Structure Prediction (CASP), 41, 91

Critical Assessment of Techniques for Free Energy Evaluation (CATFEE), 41, 91

Critical lipophilicity, 233

Critical micelle concentration, 232 Critical state of association, 235 Cross-docking experiments, 41 Crossing point, 190

Crystal disruption, 226 Crystallography books, 289, 319 Curve crossings, 187, 191 Cyclin, 67, 68

Cyclin-dependent kinase, 2, 67, 68 Cytochrome, 82

Darwin corrections, 159 Databases, v, 3, 82, 259 Davidson method, 168 db_translate, 36

De novo ligand design, 2, 4, 11, 22, 23, 28, 31 Dead-end elimination (DEE), 20

Decoy complexes, 91 Degenerate states, 171

DelPhi, 42, 77

Demixing of immiscible liquids, 216 Derivatives, 161

Desolvation, 27 Desolvation energies, 70, 88

Deterministic cellular automata, 213 Deterministic rules, 209

Dielectric constant, 26, 27, 28, 72, 77, 224 Diffusion, 224, 228, 232

Digital computers, 209 Dihedral angle space, 86

Dihydrofolate reductase (DHFR), 25, 39

DING HAO, 249

Dipolar spin-spin coupling operators, 147 Dipole moments, 182

Dirac theory, 107, 109, 124, 125 Dirac-Coulomb-Breit operator, 124 Direct methods, 168

Discontinuous microscopic events, 206 Discrete water molecules, 14 Disorder-order transition, 67 Dissociation constants, 63 Dissociation energy, 187

Dissociation rates, 63

Dissociative electronic state, 190 Dissolution, 226

Distance compatibility, 6, 18 Distance geometry methods, 11, 18 Distance matrix, 18

Distribution, 38 Dithiosuccinimide, 183

DNA dodecamer-netropsin complex, 39 DOCK, 2, 4, 6, 7, 19, 25, 26, 32, 33, 34, 35,

38, 43, 78

Docked conformations, 26 Docking, x, 1, 37, 61, 69, 70, 90 Docking programs, 2, 4, 29

DOT, 77

Double excitations, 128, 129, 130 Double groups, 140, 143, 158, 194

DREAM++, 23

Dressed Hamiltonians, 195 Drug, 45

Drug design, 21, 62

Drug discovery, 1, 37, 45, 221

Drug-like molecules, 3, 10, 11, 38, 39, 44 Drug-receptor encounters, 221 DrugScore, 33

Dynamic correlation effects, 195 Dynamic properties, 66

ECEPP/3 force field, 18

Effective core potentials (ECP), 136, 193, 194 Effective one-electron spin-orbit Hamiltonians,

132

Effective potential, 162 Eigenvalues, 116 Eigenvectors, 118 Electric dipole, 186

Electric dipole transitions, 105, 181 Electron correlation, 127, 159, 167 Electron spin, 101, 103, 108 Electron spin resonance (ESR), 100 Electronic spin-spin coupling, 147 Electronic states, 126, 170 Electrostatic calculations, 42 Electrostatic complementarity, 26 Electrostatic continuum, 26 Electrostatic energies, 170 Electrostatic interactions, 65, 72 Electrostatic solvation, 18 Electrostriction, 224

Emergent properties, 221

Empirical atomic hydrophobicities, 25, 26 Empirical one-electron operators, 132 Empirical scoring functions, 24, 28, 29, 34 Empiricism, 206