Exploring the role of receptor flexibility in structure-based drug discovery

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Trott, O., & Olson, A. J. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21334 · Cited by 38,412 · see citing works

Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., et al. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm0306430 · Cited by 10,057 · see citing works

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.

Monod, J., Wyman, J., & Changeux, J. (1965) · Journal of Molecular Biology · doi:10.1016/s0022-2836(65)80285-6 · Cited by 7,681 · see citing works

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling

Torrie, G. M., & Valleau, J. P. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90121-8 · Cited by 6,091 · see citing works

Escaping free-energy minima

Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626 · see citing works

Replica-exchange molecular dynamics method for protein folding

Sugita, Y., & Okamoto, Y. (1999) · Chemical Physics Letters · doi:10.1016/s0009-2614(99)01123-9 · Cited by 4,499 · see citing works

Docking and scoring in virtual screening for drug discovery: methods and applications

Kitchen, D. B., Decornez, H. Y., Furr, J. R., & Bajorath, J. (2004) · Nature Reviews Drug Discovery · doi:10.1038/nrd1549 · Cited by 4,245 · see citing works

Essential dynamics of proteins

Amadei, A., Linssen, A. B. M., & Berendsen, H. J. C. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340170408 · Cited by 3,487 · see citing works

Molecular dynamics simulations of biomolecules

Karplus, M., & McCammon, J. (2002) · Nature Structural Biology · doi:10.1038/nsb0902-646 · Cited by 3,401 · see citing works

Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits *

Koshland, D. E., Némethy, G., & Filmer, D. (1966) · Biochemistry · doi:10.1021/bi00865a047 · Cited by 3,019 · see citing works

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

Hou, T., Wang, J., Li, Y., & Wang, W. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci100275a · Cited by 2,800 · see citing works

Allosteric proteins and cellular control systems

Monod, J., Changeux, J., & Jacob, F. (1963) · Journal of Molecular Biology · doi:10.1016/s0022-2836(63)80091-1 · Cited by 2,240 · see citing works

Application of a Theory of Enzyme Specificity to Protein Synthesis.

Koshland, D. (1958) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.44.2.98 · Cited by 2,140 · see citing works

The role of dynamic conformational ensembles in biomolecular recognition

Boehr, D. D., Nussinov, R., & Wright, P. E. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.232 · Cited by 2,008 · see citing works

How fast-folding proteins fold

Lindorff-Larsen, K., Piana, S., Dror, R. O., & Shaw, D. E. (2011) · Science · doi:10.1126/science.1208351 · Cited by 1,980 · see citing works

Dynamics of folded proteins

McCammon, J., Gelin, B., & Karplus, M. (1977) · Nature · doi:10.1038/267585a0 · Cited by 1,972 · see citing works

Atomic-level characterization of the structural dynamics of proteins

Shaw, D. E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R. O., Eastwood, M. P., Bank, J. A., Jumper, J. M., Salmon, J. K., Shan, Y., et al. (2010) · Science · doi:10.1126/science.1187409 · Cited by 1,923 · see citing works

A Critical Assessment of Docking Programs and Scoring Functions

Warren, G. L., Andrews, C. W., Capelli, A., Clarke, B., LaLonde, J. M., Lambert, M. H., Lindvall, M., Nevins, N., Semus, S. F., Senger, S., et al. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm050362n · Cited by 1,840 · see citing works

The Many Roles of Computation in Drug Discovery

Jorgensen, W. L. (2004) · Science · doi:10.1126/science.1096361 · Cited by 1,560 · see citing works

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules

Hamelberg, D., Mongan, J., & McCammon, J. A. (2004) · The Journal of Chemical Physics · doi:10.1063/1.1755656 · Cited by 1,536 · see citing works

Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid

Torrie, G. M., & Valleau, J. P. (1974) · Chemical Physics Letters · doi:10.1016/0009-2614(74)80109-0 · Cited by 1,446 · see citing works

Virtual screening of chemical libraries

Shoichet, B. K. (2004) · Nature · doi:10.1038/nature03197 · Cited by 1,425 · see citing works

Molecular dynamics simulations and drug discovery

Durrant, J. D., & McCammon, J. A. (2011) · BMC Biology · doi:10.1186/1741-7007-9-71 · Cited by 1,412 · see citing works

Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins

Adcock, S. A., & McCammon, J. A. (2006) · Chemical Reviews · doi:10.1021/cr040426m · Cited by 1,279 · see citing works

Metadynamics

Barducci, A., Bonomi, M., & Parrinello, M. (2011) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.31 · Cited by 1,217 · see citing works

Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

Gohlke, H., Kiel, C., & Case, D. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00610-7 · Cited by 1,087 · see citing works

Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders

Jeffrey Conn, P., Christopoulos, A., & Lindsley, C. W. (2009) · Nature Reviews Drug Discovery · doi:10.1038/nrd2760 · Cited by 1,063 · see citing works

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

Lange, O. F., Lakomek, N., Farès, C., Schroeder, G. F., Walter, K. F. A., Becker, S., Meiler, J., Grubmüller, H., Griesinger, C., & de Groot, B. L. (2008) · Science · doi:10.1126/science.1157092 · Cited by 1,044 · see citing works

Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding

Massova, I., & Kollman, P. A. (2000) · Perspectives in Drug Discovery and Design · doi:10.1023/a:1008763014207 · Cited by 1,015 · see citing works

Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA

Rastelli, G., Río, A. D., Degliesposti, G., & Sgobba, M. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21372 · Cited by 838 · see citing works

Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf

Gohlke, H., & Case, D. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.10379 · Cited by 836 · see citing works

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

Csermely, P., Palotai, R., & Nussinov, R. (2010) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2010.04.009 · Cited by 821 · see citing works

Structure and dynamics of the M3 muscarinic acetylcholine receptor

Kruse, A. C., Hu, J., Pan, A. C., Arlow, D. H., Rosenbaum, D. M., Rosemond, E., Green, H. F., Liu, T., Chae, P. S., Dror, R. O., et al. (2012) · Nature · doi:10.1038/nature10867 · Cited by 812 · see citing works

The Dynamic Process of β2-Adrenergic Receptor Activation

Nygaard, R., Zou, Y., Dror, R. O., Mildorf, T. J., Arlow, D. H., Manglik, A., Pan, A. C., Liu, C. W., Fung, J. J., Bokoch, M. P., et al. (2013) · Cell · doi:10.1016/j.cell.2013.01.008 · Cited by 797 · see citing works

Large-amplitude nonlinear motions in proteins

Garcı́a, A. E. (1992) · Physical Review Letters · doi:10.1103/physrevlett.68.2696 · Cited by 788 · see citing works

New Tools Provide New Insights in NMR Studies of Protein Dynamics

Mittermaier, A., & Kay, L. E. (2006) · Science · doi:10.1126/science.1124964 · Cited by 785 · see citing works

Allostery in Disease and in Drug Discovery

Nussinov, R., & Tsai, C. (2013) · Cell · doi:10.1016/j.cell.2013.03.034 · Cited by 764 · see citing works

Implications of protein flexibility for drug discovery

Teague, S. J. (2003) · Nature Reviews Drug Discovery · doi:10.1038/nrd1129 · Cited by 755 · see citing works

Long-timescale molecular dynamics simulations of protein structure and function

Klepeis, J. L., Lindorff‐Larsen, K., Dror, R. O., & Shaw, D. E. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.03.004 · Cited by 750 · see citing works

Allostery without conformational change

Cooper, A., & Dryden, D. T. F. (1984) · European Biophysics Journal · doi:10.1007/bf00276625 · Cited by 740 · see citing works

Use of an Induced Fit Receptor Structure in Virtual Screening

Sherman, W., Beard, H. S., & Farid, R. (2005) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2005.00327.x · Cited by 703 · see citing works

Allosteric Modulation of G Protein–Coupled Receptors

May, L. T., Leach, K., Sexton, P. M., & Christopoulos, A. (2006) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.47.120505.105159 · Cited by 698 · see citing works

Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin

Elber, R., & Karplus, M. (1987) · Science · doi:10.1126/science.3798113 · Cited by 673 · see citing works

Virtual ligand screening: strategies, perspectives and limitations

Klebe, G. (2006) · Drug Discovery Today · doi:10.1016/j.drudis.2006.05.012 · Cited by 669 · see citing works

Allosteric binding sites on cell-surface receptors: novel targets for drug discovery

Christopoulos, A. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd746 · Cited by 665 · see citing works

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

Buch, I., Giorgino, T., & De Fabritiis, G. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1103547108 · Cited by 655 · see citing works

Efficient Drug Lead Discovery and Optimization

Jorgensen, W. L. (2009) · Accounts of Chemical Research · doi:10.1021/ar800236t · Cited by 651 · see citing works

Folding funnels, binding funnels, and protein function

Tsai, C., Kumar, S., Ma, B., & Nussinov, R. (1999) · Protein Science · doi:10.1110/ps.8.6.1181 · Cited by 648 · see citing works

Discovery of Raltegravir, a Potent, Selective Orally Bioavailable HIV-Integrase Inhibitor for the Treatment of HIV-AIDS Infection

Summa, V., Petrocchi, A., Bonelli, F., Crescenzi, B., Donghi, M., Ferrara, M., Fiore, F., Gardelli, C., Paz, O. G., Hazuda, D. J., et al. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm800245z · Cited by 636 · see citing works

Unfolded Proteins and Protein Folding Studied by NMR

Dyson, H. J., & Wright, P. E. (2004) · Chemical Reviews · doi:10.1021/cr030403s · Cited by 628 · see citing works

How Does a Drug Molecule Find Its Target Binding Site?

Shan, Y., Kim, E. T., Eastwood, M. P., Dror, R. O., Seeliger, M. A., & Shaw, D. E. (2011) · Journal of the American Chemical Society · doi:10.1021/ja202726y · Cited by 614 · see citing works

Folding funnels and binding mechanisms

Ma, B., Kumar, S., Tsai, C.-J., & Nussinov, R. (1999) · Protein Engineering, Design and Selection · doi:10.1093/protein/12.9.713 · Cited by 594 · see citing works

Biomolecular Modeling: Goals, Problems, Perspectives

A, W. F. V. G., Bakowies, D., Baron, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P. J., Geerke, D. P., Glättli, A., Hünenberger, P. H., et al. (2006) · Angewandte Chemie International Edition · doi:10.1002/anie.200502655 · Cited by 562 · see citing works

Alchemical free energy methods for drug discovery: Progress and challenges

Chodera, J., Mobley, D., Shirts, M., Dixon, R. W., Branson, K., & Pande, V. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.01.011 · Cited by 545 · see citing works

Accelerating molecular dynamic simulation on graphics processing units

Friedrichs, M. S., Eastman, P. K., Vaidyanathan, V., Houston, M., LeGrand, S., Beberg, A. L., Ensign, D. L., Bruns, C. M., & Pande, V. S. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21209 · Cited by 529 · see citing works

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

Pierce, L., Salomón–Ferrer, R., de Oliveira, C. A. F., McCammon, J. A., & Walker, R. C. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300284c · Cited by 515 · see citing works

ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility

Meiler, J., & Baker, D. A. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21086 · Cited by 508 · see citing works

Flexible ligand docking to multiple receptor conformations: a practical alternative

Totrov, M., & Abagyan, R. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.01.004 · Cited by 497 · see citing works

Virtual screening strategies in drug discovery

McInnes, C. (2007) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2007.08.033 · Cited by 469 · see citing works

Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques

Brenke, R., Kozakov, D., Chuang, G., Beglov, D., Hall, D. R., Landon, M. R., Mattos, C., & Vajda, S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp036 · Cited by 460 · see citing works

Ligand-receptor interactions

Tembre, B. L., & McCammon, J. A. (1984) · Computers & Chemistry · doi:10.1016/0097-8485(84)85020-2 · Cited by 459 · see citing works

RosettaLigand Docking with Full Ligand and Receptor Flexibility

Davis, I., & Baker, D. A. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.11.010 · Cited by 438 · see citing works

ON THE COOPERATIVITY OF BIOLOGICAL MEMBRANES

Changeux, J., Thiéry, J., Tung, Y., & KITTEL, C. (1967) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.57.2.335 · Cited by 434 · see citing works

Collective protein dynamics in relation to function

Berendsen, H. J. C. (2000) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00061-0 · Cited by 425 · see citing works

Multiscale modeling of biomolecular systems: in serial and in parallel

Ayton, G. S., Noid, W. G., & Voth, G. A. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.03.004 · Cited by 420 · see citing works

Principal Component Analysis and Long Time Protein Dynamics

Balsera, M., Wriggers, W. R., Oono, Y., & Schulten, K. J. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp9536920 · Cited by 417 · see citing works

“Soft docking”: Matching of molecular surface cubes

Jiang, F., & Kim, S. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90859-5 · Cited by 407 · see citing works

Molecular docking to ensembles of protein structures 1 1Edited by B. Honig

Knegtel, R. M. A., Kuntz, I. D., & Oshiro, C. M. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0776 · Cited by 393 · see citing works

Allostery and the Monod-Wyman-Changeux Model After 50 Years

Changeux, J. (2012) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-050511-102222 · Cited by 393 · see citing works

The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum

Kitao, A., Hirata, F., & Gō, N. (1991) · Chemical Physics · doi:10.1016/0301-0104(91)87082-7 · Cited by 392 · see citing works

Terpene Biosynthesis: Modularity Rules

Oldfield, E., & Lin, F. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.201103110 · Cited by 392 · see citing works

Basic ingredients of free energy calculations: A review

Christ, C. D., Mark, A. E., & A, W. F. V. G. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21450 · Cited by 391 · see citing works

Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme

Lin, J., Perryman, A. L., Schames, J. R., & McCammon, J. A. (2002) · Journal of the American Chemical Society · doi:10.1021/ja0260162 · Cited by 386 · see citing works

Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state

Tobi, D., & Bahar, İ. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507603102 · Cited by 380 · see citing works

Folding and binding cascades: Shifts in energy landscapes

Tsai, C.-J., Ma, B., & Nussinov, R. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.18.9970 · Cited by 365 · see citing works

Ligand docking to proteins with discrete side-chain flexibility

Leach, A. R. (1994) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80038-5 · Cited by 363 · see citing works

Discovery of a Novel Binding Trench in HIV Integrase

Schames, J. R., Henchman, R. H., Siegel, J. S., Sotriffer, C., Ni, H., & McCammon, J. A. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm0341913 · Cited by 354 · see citing works

Water Networks Contribute to Enthalpy/Entropy Compensation in Protein–Ligand Binding

Breiten, B., Lockett, M. R., Sherman, W., Fujita, S., Al-Sayah, M. H., Lange, H., Bowers, C. M., Heroux, A., Krilov, G., & Whitesides, G. M. (2013) · Journal of the American Chemical Society · doi:10.1021/ja4075776 · Cited by 341 · see citing works

The Oxygen Equilibrium of Hemoglobin and Its Structural Interpretation

Pauling, L. C. (1935) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.21.4.186 · Cited by 340 · see citing works

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

Amaro, R. E., Baron, R., & McCammon, J. A. (2008) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-007-9159-2 · Cited by 321 · see citing works

Protein flexibility and drug design: how to hit a moving target

Carlson, H. A. (2002) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(02)00341-1 · Cited by 314 · see citing works

Water in Cavity−Ligand Recognition

Baron, R., Setny, P., & McCammon, J. A. (2010) · Journal of the American Chemical Society · doi:10.1021/ja1050082 · Cited by 275 · see citing works

Conformational selection or induced fit? 50 years of debate resolved

Changeux, J., & Edelstein, S. J. (2011) · F1000 Biology Reports · doi:10.3410/b3-19 · Cited by 272 · see citing works

Allostery at G Protein-Coupled Receptor Homo- and Heteromers: Uncharted Pharmacological Landscapes

Smith, N. J., & Milligan, G. (2010) · Pharmacological Reviews · doi:10.1124/pr.110.002667 · Cited by 261 · see citing works

A Monte Carlo method for obtaining the interionic potential of mean force in ionic solution

Patey, G. N., & Valleau, J. P. (1975) · The Journal of Chemical Physics · doi:10.1063/1.431685 · Cited by 242 · see citing works

Soft Docking and Multiple Receptor Conformations in Virtual Screening

Ferrari, A. M., Wei, B. Q., Costantino, L., & Shoichet, B. K. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm049756p · Cited by 239 · see citing works

Managing protein flexibility in docking and its applications

B‐Rao, C., Subramanian, J., & Sharma, S. (2009) · Drug Discovery Today · doi:10.1016/j.drudis.2009.01.003 · Cited by 233 · see citing works

Perspective: Alchemical free energy calculations for drug discovery.

Mobley, D., & Klimovich, P. V. (2012) · Journal of Chemical Physics · doi:10.1063/1.4769292 · Cited by 232 · see citing works

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

Limongelli, V., Bonomi, M., Marinelli, L., Gervasio, F. L., Cavalli, A., Novellino, E., & Parrinello, M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913377107 · Cited by 226 · see citing works

Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53

Wassman, C. D., Baronio, R., Demir, Ö., Wallentine, B. D., Chen, C.-K., Hall, L., Salehi, F., Lin, D., Chung, B. P., Hatfield, G. W., et al. (2013) · Nature Communications · doi:10.1038/ncomms2361 · Cited by 223 · see citing works

Activation and dynamic network of the M2 muscarinic receptor

Miao, Y., Nichols, S. E., Gasper, P. M., Metzger, V. T., & McCammon, J. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1309755110 · Cited by 217 · see citing works

Molecular simulation as an aid to experimentalists

van Gunsteren, W. F., Dolenc, J., & Mark, A. E. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.12.007 · Cited by 205 · see citing works

Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures

Barril, X., & Morley, S. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm048972v · Cited by 196 · see citing works

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

Włodarski, T., & Žagrović, B. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906966106 · Cited by 194 · see citing works

Molecular recognition and ligand association.

Baron, R., & McCammon, J. (2013) · Annual review of physical chemistry (Print) · doi:10.1146/annurev-physchem-040412-110047 · Cited by 190 · see citing works

Allostery and population shift in drug discovery

Kar, G., Keskin, Ö., Gürsoy, A., & Nussinov, R. (2010) · Current Opinion in Pharmacology · doi:10.1016/j.coph.2010.09.002 · Cited by 190 · see citing works

Bisphosphonates target multiple sites in both cis - and trans -prenyltransferases

Guo, R., Cao, R., Liang, P., Ko, T., Chang, T.-H., Hudock, M. P., Jeng, W. Y., Chen, C. K.-M., Zhang, Y., Song, Y., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702254104 · Cited by 186 · see citing works

Molecular Recognition by Induced Fit: How Fit is the Concept?

Bosshard, H. R. (2001) · Physiology · doi:10.1152/physiologyonline.2001.16.4.171 · Cited by 184 · see citing works

Taming the complexity of protein folding

Bowman, G., Voelz, V. A., & Pande, V. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.10.006 · Cited by 181 · see citing works

A Flexible Approach to Induced Fit Docking

Nabuurs, S. B., Wagener, M., & de Vlieg, J. (2007) · Journal of Medicinal Chemistry · doi:10.1021/jm070593p · Cited by 179 · see citing works

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

Rueda, M., Bottegoni, G., & Abagyan, R. A. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci9003943 · Cited by 176 · see citing works

Studying functional dynamics in bio-molecules using accelerated molecular dynamics

Markwick, P. R. L., & McCammon, J. A. (2011) · Physical Chemistry Chemical Physics · doi:10.1039/c1cp22100k · Cited by 171 · see citing works

Protein flexibility in docking and surface mapping

Lexa, K. W., & Carlson, H. A. (2012) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583512000066 · Cited by 168 · see citing works

Exploring Multiple Timescale Motions in Protein GB3 Using Accelerated Molecular Dynamics and NMR Spectroscopy

Markwick, P. R. L., Bouvignies, G., & Blackledge, M. J. (2007) · Journal of the American Chemical Society · doi:10.1021/ja0687668 · Cited by 164 · see citing works

Crystal structure of cis -prenyl chain elongating enzyme, undecaprenyl diphosphate synthase

Fujihashi, M., Zhang, Y., Higuchi, Y., Li, X.-Y., Koyama, T., & Miki, K. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.071514398 · Cited by 163 · see citing works

Biomolecular simulations at constant pH

Mongan, J., & Case, D. A. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.02.002 · Cited by 158 · see citing works

Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time?

Shirts, M., Mobley, D., & Chodera, J. (2007) · Annual reports in computational chemistry · doi:10.1016/s1574-1400(07)03004-6 · Cited by 157 · see citing works

Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities

Gasper, P. M., Fuglestad, B., Komives, E. A., Markwick, P. R. L., & McCammon, J. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218414109 · Cited by 154 · see citing works

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

Wereszczynski, J., & McCammon, J. (2011) · Quarterly Reviews of Biophysics (print) · doi:10.1017/s0033583511000096 · Cited by 152 · see citing works

Theory of biomolecular recognition

McCammon, J. A. (1998) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(98)80046-8 · Cited by 150 · see citing works

Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin

Biela, A., Nasief, N. N., Betz, M., Heine, A., Hangauer, D. G., & Klebe, G. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201208561 · Cited by 149 · see citing works

An improved method to predict the entropy term with the MM/PBSA approach

Kongsted, J., & Ryde, U. (2008) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-008-9238-z · Cited by 145 · see citing works

Is it the shape of the cavity, or the shape of the water in the cavity?

Snyder, P. W., Lockett, M. R., Moustakas, D. T., & Whitesides, G. M. (2013) · The European Physical Journal Special Topics · doi:10.1140/epjst/e2013-01818-y · Cited by 141 · see citing works

Targeting Isoprenoid Biosynthesis for Drug Discovery: Bench to Bedside

Oldfield, E. (2010) · Accounts of Chemical Research · doi:10.1021/ar100026v · Cited by 130 · see citing works

Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery

Jahnke, W., Rondeau, J., Cotesta, S., Marzinzik, A. L., Pellé, X., Geiser, M., Strauss, A., Götte, M., Bitsch, F., Hemmig, R., et al. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.421 · Cited by 129 · see citing works

Computational Drug Discovery and Design

Baron, R. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-465-0 · Cited by 128 · see citing works

A statistical analysis of the precision of reweighting-based simulations

Shen, T., & Hamelberg, D. (2008) · The Journal of Chemical Physics · doi:10.1063/1.2944250 · Cited by 126 · see citing works

Computationally-Guided Optimization of a Docking Hit to Yield Catechol Diethers as Potent Anti-HIV Agents

Bollini, M., Domaoal, R. A., Thakur, V. V., Gallardo‐Macias, R., Spasov, K. A., Anderson, K. S., & Jorgensen, W. L. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm201134m · Cited by 119 · see citing works

Structure-based computational analysis of protein binding sites for function and druggability prediction

Nisius, B., Sha, F., & Gohlke, H. (2011) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2011.12.005 · Cited by 114 · see citing works

Mapping the Druggable Allosteric Space of G‐Protein Coupled Receptors: a Fragment‐Based Molecular Dynamics Approach

Ivetac, A., & McCammon, J. A. (2010) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2010.01012.x · Cited by 111 · see citing works

Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer‐Aided Drug Design

Sinko, W., Lindert, S., & McCammon, J. A. (2012) · Chemical Biology & Drug Design · doi:10.1111/cbdd.12051 · Cited by 111 · see citing works

Antibacterial drug leads targeting isoprenoid biosynthesis

Zhu, W., Zhang, Y., Sinko, W., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219899110 · Cited by 108 · see citing works

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles

Fenwick, R. B., Esteban-Martín, S., & Salvatella, X. (2011) · European Biophysics Journal · doi:10.1007/s00249-011-0754-8 · Cited by 106 · see citing works

Emerging Methods for Ensemble-Based Virtual Screening

Amaro, R. E., & Li, W. W. (2010) · Current Topics in Medicinal Chemistry · doi:10.2174/156802610790232279 · Cited by 106 · see citing works

Advances in all atom sampling methods for modeling protein–ligand binding affinities

Gallicchio, E., & Levy, R. M. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.01.010 · Cited by 101 · see citing works

Computational Prediction of Protein Hot Spot Residues

Morrow, J. K., & Zhang, S. (2012) · Current Pharmaceutical Design · doi:10.2174/138161212799436412 · Cited by 98 · see citing works

Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir

Lawrenz, M., Baron, R., & McCammon, J. A. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct800559d · Cited by 91 · see citing works

Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening

Nichols, S. E., Baron, R., Ivetac, A., & McCammon, J. A. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200117n · Cited by 91 · see citing works

50th anniversary of the word “allosteric”

Changeux, J. (2011) · Protein Science · doi:10.1002/pro.658 · Cited by 84 · see citing works

Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols

Osguthorpe, D. J., Sherman, W., & Hagler, A. T. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp3003992 · Cited by 75 · see citing works

Toward an atomistic description of the urea-denatured state of proteins

Candotti, M., Esteban-Martín, S., Salvatella, X., & Orozco, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1216589110 · Cited by 65 · see citing works

Allo-Network Drugs: Extension of the Allosteric Drug Concept to Protein- Protein Interaction and Signaling Networks

Szilágyi, A., Nussinov, R., & Csermely, P. (2013) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026611313010007 · Cited by 65 · see citing works

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations

Wereszczynski, J., & McCammon, J. A. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct100322t · Cited by 57 · see citing works

Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations

Wereszczynski, J., & McCammon, J. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1117441109 · Cited by 56 · see citing works

Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods

Lee, H. S., Choi, J., Kufareva, I., et al. (2008) · Journal of Chemical Information and Modeling · doi:10.1021/ci700376c · Cited by 54 · see citing works

Conformational Selection in G-Proteins: Lessons from Ras and Rho

Grant, B. J., McCammon, J. A., & Gorfe, A. A. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.10.020 · Cited by 54 · see citing works

Computer-Aided Identification ofTrypanosoma bruceiUridine Diphosphate Galactose 4′-Epimerase Inhibitors: Toward the Development of Novel Therapies for African Sleeping Sickness

Durrant, J. D., Urbaniak, M. D., Ferguson, M. A. J., et al. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm100456a · Cited by 54 · see citing works

Receptor flexibility in small‐molecule docking calculations

Kokh, D. B., Wade, R. C., & Wenzel, W. (2011) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.29 · Cited by 54 · see citing works

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations

de Oliveira, C. A. F., Hamelberg, D., & McCammon, J. A. (2008) · Journal of Chemical Theory and Computation · doi:10.1021/ct800160q · Cited by 53 · see citing works

Non‐Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer‐Aided Drug Design

Durrant, J. D., Cao, R., Gorfe, A. A., et al. (2011) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2011.01164.x · Cited by 52 · see citing works

The Dynamic Structure of Thrombin in Solution

Fuglestad, B., Gasper, P. M., Tonelli, M., et al. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.05.047 · Cited by 52 · see citing works

Oxygen-organophosphate linkage in hemoglobin A. The double hump effect

KISTER, J., Poyart, C., & Edelstein, S. J. (1987) · Biophysical Journal · doi:10.1016/s0006-3495(87)83242-3 · Cited by 47 · see citing works

Farnesyl Diphosphate Synthase Inhibitors fromIn SilicoScreening

Lindert, S., Zhu, W., Liu, Y., et al. (2013) · Chemical Biology & Drug Design · doi:10.1111/cbdd.12121 · Cited by 46 · see citing works

Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study

Williams, S., Blachly, P. G., & McCammon, J. A. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23136 · Cited by 43 · see citing works

Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand‐bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target

Sinko, W., de Oliveira, C. A. F., Williams, S., Wynsberghe, A. W. V., Durrant, J. D., Cao, R., Oldfield, E., & McCammon, J. A. (2011) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2011.01101.x · Cited by 41 · see citing works

Evolutionary profiles from the QR factorization of multiple sequence alignments

Sethi, A., O’Donoghue, P., & Luthey-Schulten, Z. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409715102 · Cited by 39 · see citing works

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

Sinko, W., de Oliveira, C. A. F., Pierce, L., et al. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct200615k · Cited by 38 · see citing works

Accelerated molecular dynamics in computational drug design.

Wereszczynski, J., & McCammon, J. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-465-0_30 · Cited by 28 · see citing works

Synergistic use of NMR and MD simulations to study the structural heterogeneity of proteins

Esteban-Martín, S., Fenwick, R. B., & Salvatella, X. (2012) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1093 · Cited by 26 · see citing works

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

(2013) · Springer series in bio-/neuroinformatics · doi:10.1007/978-3-642-28554-7 · Cited by 25 · see citing works

Rational Prediction with Molecular Dynamics for Hit Identification

Nichols, S. E., Swift, R. V., & Amaro, R. E. (2012) · Current Topics in Medicinal Chemistry · doi:10.2174/156802612804910313 · Cited by 23 · see citing works

Structural and Entropic Allosteric Signal Transduction Strength via Correlated Motions

Long, D., & Brüschweiler, R. (2012) · The Journal of Physical Chemistry Letters · doi:10.1021/jz300488e · Cited by 20 · see citing works

Expanding the Conformational Selection Paradigm in Protein-Ligand Docking

Kuzu, G., Keskin, Ö., Gürsoy, A., & Nussinov, R. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-465-0_5 · Cited by 15 · see citing works

Enhanced Sampling for Biomolecular Simulations

Berhanu, W. M., Jiang, P., & Hansmann, U. H. E. (2013) · Springer series in bio-/neuroinformatics · doi:10.1007/978-3-642-28554-7_8 · Cited by 4 · see citing works

USA: Going public on rights

Norman, C. A. (1977) · Nature · doi:10.1038/267006a0 · Cited by 1 · see citing works

Supramolecular Architecture of Rhodopsin in Native Photoreceptors Revealed by Cryo-Electron Tomography

Gunkel, M., Kaupp, U. B., & Al‐Amoudi, A. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2012.11.184 · Cited by 1 · see citing works

Enhanced Conformational Sampling of M2 Muscarinic Acetylcholine Receptor for Designing Selective Allosteric Drugs

Miao, Y., & McCammon, J. A. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2012.11.182 · Cited by 1 · see citing works

Role of computer-aided drug design in modern drug discovery

Macalino, S. J. Y., Gosu, V., Hong, S., & Choi, S. (2015) · Archives of Pharmacal Research · doi:10.1007/s12272-015-0640-5 · Cited by 762 · see citing works

Biomolecular simulations: from dynamics and mechanisms to computational assays of biological activity

Huggins, D. J., Biggin, P. C., Dämgen, M. A., Essex, J. W., Harris, S. A., Henchman, R. H., Khalid, S., Kuzmanic, A., Laughton, C. A., Michel, J., et al. (2019) · WIREs Computational Molecular Science · doi:10.1002/wcms.1393 · Cited by 169 · see citing works

Understanding the challenges of protein flexibility in drug design.

Antunes, D. A., Devaurs, D., & Kavraki, L. E. (2015) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2015.1094458 · Cited by 131 · see citing works

Modeling the binding of diverse ligands within the Ah receptor ligand binding domain

Giani Tagliabue, S., Faber, S. C., Motta, S., Denison, M. S., & Bonati, L. (2019) · Scientific Reports · doi:10.1038/s41598-019-47138-z · Cited by 106 · see citing works

Protein flexibility in drug discovery: from theory to computation.

Buonfiglio, R., Recanatini, M., & Masetti, M. (2015) · ChemMedChem · doi:10.1002/cmdc.201500086 · Cited by 73 · see citing works

Mechanisms of ligand binding

Di Cera, E. (2020) · Biophysics Reviews · doi:10.1063/5.0020997 · Cited by 73 · see citing works

Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms

Bonati, L., Corrada, D., Giani Tagliabue, S., & Motta, S. (2017) · Current Opinion in Toxicology · doi:10.1016/j.cotox.2017.01.011 · Cited by 27 · see citing works

Hierarchical virtual screening approaches in small molecule drug discovery

Kumar, A., & Zhang, K. Y. J. (2014) · Methods · doi:10.1016/j.ymeth.2014.07.007 · Cited by 157 · see citing works

[Research progress of virtual screening aided drug discovery].

Liu, A., & Du, G. (2009) · PubMed · Cited by 5 · see citing works

Structure-based Virtual Screening Approaches in Kinase-directed Drug Discovery

Bajusz, D., Ferenczy, G. G., & Keserű, G. M. (2017) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026617666170224121313 · Cited by 88 · see citing works

Deep Learning for Ligand-Based Virtual Screening in Drug Discovery

Bahi, M., & Batouche, M. (2018) · International Conference on Pattern Analysis and Intelligent Systems (PAIS) · doi:10.1109/pais.2018.8598488 · Cited by 46 · see citing works

Ensemble-based virtual screening of African natural products to target human thymidylate synthase

Mteremko, D., Chilongola, J. O., Paluch, A. S., & Chacha, M. N. (2023) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2023.108568 · Cited by 2 · see citing works