MMTSB - Publications

	2005

	Manuscripts in Press

	DA Case, T Cheatham, T Darden, H Gohlke, R Luo, KM Merz, Jr., A Onufriev, C Simmerling, B Wang and R Woods The Amber Biomolecular Simulation Programs Journal of Computational Chemistry, 2005, in the press .

	S Falke, F Tama, CL Brooks, III, EP Gogol and MT Fisher The 13 A Structure of a Chaperonin GroEL-Protein Substrate complex by Cryo-Electron Microscopy Journal of Molecular Biology, 2005, in the press .

	Journal Articles

	E Bindewald and J Skolnick A scoring function for docking ligands to low-resolution protein structures Journal of Computational Chemistry, 2005, 26 (4), 374-83. PubMed

	J Chen, HS Won, W Im, HJ Dyson and CL Brooks, III Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling J Biomol NMR, 2005, 31 (1), 59-64. PubMed

	CM Shepherd and VS Reddy Extent of protein-protein interactions and quasi-equivalence in viral capsids Proteins: Structure, Function, and Bioinformatics, 2005, 58 (2), 472-7. PubMed

	F Tama and CL Brooks, III Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis Journal of Molecular Biology, 2005, 345 (2), 299-314. PubMed

	F Tama, M Feig, J Liu, CL Brooks, III and KA Taylor The Requirement for Mechanical Coupling Between Head and S2 Domains in Smooth Muscle Myosin ATPase Regulation and its Implications for Dimeric Motor Function Journal of Molecular Biology, 2005, 345 (4), 837-854. PubMed

	Book Chapters

	JA Mears, SM Stagg and SC Harvey Modeling of Very Large RNA Assemblies Using Reduced Representations Handbook of RNA Biochemistry, 2005, E Westhof, S Binereif, A Schšn andR Hartmann, Wiley-VCH, Weinheim, Pgs .

	Conference Proceedings

	M Taufer, C An, A Kerstens and CL Brooks, III Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), 2005, Denver, Colorado.

	M Taufer, D Anderson, P Cicotti and CL Brooks, III Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing 14th Heterogeneous Computing Workshop (HCW 2005), 2005, Denver, Colorado.

	Manuscripts Submitted for Publication

	J Chen, W Im and I Brooks C. L. Torsion Angle Molecular Dynamics for Efficient Sampling of Protein Conformations Journal of Computational Chemistry, 2005, submitted .

	2004

	Manuscripts in Press

	VS Reddy and JE Johnson Structure derived insights into virus assembly Advances in Virus Research, 2004, in the press .

	M Taufer, M Crowley, D Price, A Chien and CL Brooks, III Study of an Accurate and Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics Concurrency and Computation: Practice and Experience, 2004, in the press .

	Journal Articles

	J Chen, W Im and CL Brooks, III Refinement of NMR structures using implicit solvent and advanced sampling techniques Journal of the Americal Chemical Society, 2004, 126 (49), 16038-47. PubMed

	M Feig, W Im and CL Brooks, III Implicit solvation based on generalized Born theory in different dielectric environments Journal of Chemical Physics, 2004, 120 (2), 903-911 .

	M Feig, A Onufriev, MS Lee, W Im, DA Case and CL Brooks, III Performance comparison of generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures Journal of Computational Chemistry, 2004, 25 (2), 265-84. PubMed

	M Feig, J Karanicolas and CL Brooks, III MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology Journal of Molecular Graphics and Modeling, 2004, 22 (5), 377-95. PubMed

	M Feig and CL Brooks, III Recent advances in the development and application of implicit solvent models in biomolecule simulations Current Opinion in Structural Biology, 2004, 14 (2), 217-24. PubMed

	P Ferrara, H Gohlke, DJ Price, G Klebe and CL Brooks, III Assessing scoring functions for protein-ligand interactions Journal of Medicinal Chemistry, 2004, 47 (12), 3032-47. PubMed

	H Gohlke, LA Kuhn and DA Case Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach Proteins: Structure, Function, and Bioinformatics, 2004, 56 (2), 322-37. PubMed

	H Gohlke and DA Case Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf Journal of Computational Chemistry, 2004, 25 (2), 238-50. PubMed

	W Im and CL Brooks, III De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein Journal of Molecular Biology, 2004, 337 (3), 513-9. PubMed

	J Karanicolas and CL Brooks, III An evolution of minimalist models for protein folding: from the behavior of protein-like polymers to protein function Biosilico, 2004, 2 (3), 127-133 .

	A Kolinski and J Skolnick Reduced Models of Proteins and Their Applications Polymer, 2004, 45, 511-524 .

	JC LaMarque, TV Le and SC Harvey Packaging double-helical DNA into viral capsids Biopolymers, 2004, 73 (3), 348-55. PubMed

	AD MacKerell, Jr., M Feig and CL Brooks, III Improved treatment of the protein backbone in empirical force fields Journal of the Americal Chemical Society, 2004, 126 (3), 698-9. PubMed

	AD Mackerell, Jr., M Feig and CL Brooks, III Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations Journal of Computational Chemistry, 2004, 25 (11), 1400-15. PubMed

	A Natrajan, M Crowley, N Wilkins-Diehr, MA Humphrey, AD Fox, AS Grimshaw and CL Brooks, III Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion Concurrency and Computation: Practice and Experience, 2004, 16, 385-397 .

	VA Roberts, DA Case and V Tsui Predicting interactions of winged-helix transcription factors with DNA Proteins: Structure, Function, and Bioinformatics, 2004, 57 (1), 172-87. PubMed

	F Tama, O Miyashita and CL Brooks, III Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis Journal of Molecular Biology, 2004, 337 (4), 985-99. PubMed

	F Tama, O Miyashita and CL Brooks, III Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM Journal of Structural Biology, 2004, 147 (3), 315-26. PubMed

	M Tihova, KA Dryden, TV Le, SC Harvey, JE Johnson, M Yeager and A Schneemann Nodavirus coat protein imposes dodecahedral RNA structure independent of nucleotide sequence and length Journal of Virology, 2004, 78 (6), 2897-905. PubMed

	J Trylska, R Konecny, F Tama, CL Brooks, III and JA McCammon Ribosome motions modulate electrostatic properties Biopolymers, 2004, 74 (6), 423-31. PubMed

	W Wriggers, P Chacon, JA Kovacs, F Tama and S Birmanns Topology representing neural networks reconcile biomolecular shape, structure, and dynamics Neurocomputing, 2004, 56, 365-379. ISI

	Book Chapters

	ALN Rao and VS Reddy Architecture of plant viruses. Handbook of Plant Virology, 2004, JD Khan andJ Dijkstra, Haworth Press, Pgs .

	VS Reddy, P Natarajan, G Lander, C Qu, CL Brooks, III and JE Johnson Virus Particle Explorer (VIPER): A repository of virus capsid structures Conformational proteomics of macromolecular Architecture, 2004, RH Cheng andL Hammer, World Scientific Pub Co., Singapore, Pgs 403-412.

	F Tama and CL Brooks, III Unveiling molecular mechanisms of biological functions in large macromolecular assemblies using elastic network normal mode analysis Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, 2004, Q Cui andI Bahar, CRC Press, Pgs .

	Conference Proceedings

	D Kondo, M Taufer, CL Brooks, III, H Casanova and A Chien Characterizing and Evaluating Desktop Grids: An Empirical Study Proceedings of IPDPS 2004, IEEE/ACM International Parallel and Distributed Processing Symposium, 2004, Santa Fe, New Mexico.

	M Taufer, M Crowley, D Price, A Chien and CL Brooks, III Study of an Accurate and Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics Third IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004), 2004, Santa Fe, New Mexico..

	Manuscripts Submitted for Publication

	C An, TH Rod and CL Brooks, III Cis-Trans Peptidyl Prolyl Isomerization by Cyclophilin A: A Theoretical Analysis of Mechanism, Pathway, and Coupling With Enzyme Dynamics Biochemistry, 2004, submitted for publication .

	R Konecny, J Trylska, F Tama, D Zhang, NA Baker, CL Brooks, III and JA McCammon Electrostatic Properties of Cowpea Chlorotic Mottle Virus and Cucumber Mosaic Virus Capsids Proteins: Structure, Function, and Bioinformatics, 2004, submitted for publication .

	2003

	Journal Articles

	M Boniecki, P Rotkiewicz, J Skolnick and A Kolinski Protein fragment reconstruction using various modeling techniques Journal of Computer-Aided Molecular Design, 2003, 17 (11), 725-38. PubMed

	CL Brooks and DA Case Theory and simulation - The control and timescale of structure and reactivity in biological systems: from peptide folding to cellular networks - Editorial overview Current Opinion in Structural Biology, 2003, 13 (2), 143-145 .

	P Chacon, F Tama and W Wriggers Mega-Dalton biomolecular motion captured from electron microscopy reconstructions Journal of Molecular Biology, 2003, 326 (2), 485-92. PubMed

	M Feig, AD MacKerell, Jr. and CL Brooks, III Force Field Influence on the Observation of .pi.-Helical Protein Structures in Molecular Dynamics Simulations Journal of Physical Chemistry B, 2003, 107 (12), 2831-2836 .

	H Gohlke, C Kiel and DA Case Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes Journal of Molecular Biology, 2003, 330 (4), 891-913. PubMed

	H Gouda, ID Kuntz, DA Case and PA Kollman Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods Biopolymers, 2003, 68 (1), 16-34. PubMed

	SC Harvey, C Wang, S Teletchea and R Lavery Motifs in nucleic acids: molecular mechanics restraints for base pairing and base stacking Journal of Computational Chemistry, 2003, 24 (1), 1-9. PubMed

	W Im, MS Lee and CL Brooks, III Generalized Born model with a simple smoothing function Journal of Computational Chemistry, 2003, 24 (14), 1691-702. PubMed

	W Im, M Feig and CL Brooks, III An implicit membrane generalized Born theory for the study of structure, stability, and interactions of membrane proteins Biophysical Journal, 2003, 85 (5), 2900-18. PubMed

	J Karanicolas and CL Brooks, III The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design? Proceedings of the National Academy of Sciences, USA, 2003, 100 (7), 3954-9. PubMed

	J Karanicolas and CL Brooks, III Improved Go-like Models Demonstrate the Robustness of Protein Folding Mechanisms Towards Non-native Interactions Journal of Molecular Biology, 2003, 334 (2), 309-25. PubMed

	J Karanicolas and CL Brooks, III The importance of explicit chain representation in protein folding models: an examination of Ising-like models Proteins: Structure, Function, and Bioinformatics, 2003, 53 (3), 740-7. PubMed

	A Kolinski, P Klein, P Romiszowski and J Skolnick Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model Biophysical Journal, 2003, 85 (5), 3271-8. PubMed

	H Liu, C Qu, JE Johnson and DA Case Pseudo-atomic models of swollen CCMV from cryo-electron microscopy data Journal of Structural Biology, 2003, 142 (3), 356-63. PubMed

	H Lu, L Lu and J Skolnick Development of unified statistical potentials describing protein-protein interactions Biophysical Journal, 2003, 84 (3), 1895-901. PubMed

	H Lu and J Skolnick Application of statistical potentials to protein structure refinement from low resolution ab initio models Biopolymers, 2003, 70 (4), 575-84. PubMed

	YZ Ohkubo and CL Brooks, III Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A Proceedings of the National Academy of Sciences, USA, 2003, 100 (24), 13916-21. PubMed

	TH Rod, JL Radkiewicz and CL Brooks, III Correlated motion and the effect of distal mutations in dihydrofolate reductase Proceedings of the National Academy of Sciences, USA, 2003, 100 (12), 6980-5. PubMed

	C Sheldahl, J Xing, WJ Dong, SC Harvey and HC Cheung The calcium-saturated cTnI/cTnC complex: structure of the inhibitory region of cTnI Biophysical Journal, 2003, 84 (2 Pt 1), 1057-64. PubMed

	SM Stagg, JA Mears and SC Harvey A structural model for the assembly of the 30S subunit of the ribosome Journal of Molecular Biology, 2003, 328 (1), 49-61. PubMed

	F Tama, M Valle, J Frank and CL Brooks, III Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy Proceedings of the National Academy of Sciences, USA, 2003, 100 (16), 9319-23. PubMed

	V Tsui, T Macke and DA Case A novel method for finding tRNA genes Rna, 2003, 9 (5), 507-17 .

	G Wu, DH Robertson, CL Brooks, III and M Vieth Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm Journal of Computational Chemistry, 2003, 24 (13), 1549-62. PubMed

	2002

	Journal Articles

	J Arsuaga, RK Tan, M Vazquez, W Sumners de and SC Harvey Investigation of viral DNA packaging using molecular mechanics models Biophysical Chemistry, 2002, 101-102, 475-84. PubMed

	CL Brooks, III Protein and peptide folding explored with molecular simulations Accounts of Chemical Research, 2002, 35 (6), 447-54. PubMed

	P Chacon and W Wriggers Multi-resolution contour-based fitting of macromolecular structures Journal of Molecular Biology, 2002, 317 (3), 375-84. PubMed

	KV Damodaran, VS Reddy, JE Johnson and CL Brooks, III A general method to quantify quasi-equivalence in icosahedral viruses Journal of Molecular Biology, 2002, 324 (4), 723-37. PubMed

	BN Dominy and CL Brooks, III Identifying native-like protein structures using physics-based potentials Journal of Computational Chemistry, 2002, 23 (1), 147-60. PubMed

	BN Dominy, D Perl, FX Schmid and CL Brooks, III The effects of ionic strength on protein stability: the cold shock protein family Journal of Molecular Biology, 2002, 319 (2), 541-54. PubMed

	M Feig and CL Brooks, III Evaluating CASP4 predictions with physical energy functions Proteins: Structure, Function, and Genetics, 2002, 49 (2), 232-45. PubMed

	A Fiser, M Feig, CL Brooks, III and A Sali Evolution and physics in comparative protein structure modeling Accounts of Chemical Research, 2002, 35 (6), 413-21. PubMed

	J Karanicolas and CL Brooks, III The origins of asymmetry in the folding transition states of protein L and protein G Protein Science, 2002, 11 (10), 2351-61. PubMed

	MS Lee, FR Salsbury, Jr. and CL Brooks, III Novel generalized Born methods Journal of Chemical Physics, 2002, 116 (24), 10606-10614 .

	AK Mitra, G Ren, VS Reddy, A Cheng and A Froger The architecture of a water-selective pore in the lipid bilayer visualized by electron crystallography in vitreous ice Novartis Found Symp, 2002, 245, 33-46. PubMed

	DJ Price and CL Brooks, III Modern protein force fields behave comparably in molecular dynamics simulations Journal of Computational Chemistry, 2002, 23 (11), 1045-57. PubMed

	J Skolnick and A Kolinski A unified approach to the prediction of protein structure and function Advances in Chemical Physics, 2002, 120, 130-192 .

	F Tama and CL Brooks, III The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus Journal of Molecular Biology, 2002, 318 (3), 733-47. PubMed

	F Tama, W Wriggers and CL Brooks, III Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory Journal of Molecular Biology, 2002, 321 (2), 297-305. PubMed

	A Waugh, P Gendron, R Altman, JW Brown, D Case, D Gautheret, SC Harvey, N Leontis, J Westbrook, E Westhof, M Zuker and F Major RNAML: a standard syntax for exchanging RNA information Rna, 2002, 8 (6), 707-17. PubMed

	M Wojciechowski and J Skolnick Docking small ligands to low-resolution and theoretically predicated receptor structures Journal of Computational Physics, 2002, 23, 189-197 .

	X Yao, V Nguyen, W Wriggers and PA Rubenstein Regulation of yeast actin behavior by interaction of charged residues across the interdomain cleft Journal of Biological Chemistry, 2002, 277 (25), 22875-82. PubMed

	2001

	Journal Articles

	P Chacon and W Wriggers Modeling Tricks and Fitting Techniques for Multi-resolution Structures Structure, 2001, 9, 779 .

	VE Galkin, A Orlova, N Lukoyanova, W Wriggers and EH Egelman Actin Depolymerizing Factor Stabilizes an Existing State of F-actin and Can Change the Tilt of F-actin Subunits Journal of Cell Biology, 2001, 153, 75-86 .

	H Lu and J Skolnick A distance-dependent atomic knowledge-based potential for improved protein structure selection Proteins: Structure, Function, and Genetics, 2001, 44 (3), 223-32. PubMed

	WK Olson, M Bansal, SK Burley, RE Dickerson, M Gerstein, SC Harvey, U Heinemann, XJ Lu, S Neidle, Z Shakked, H Sklenar, M Suzuki, CS Tung, E Westhof, C Wolberger and HM Berman A standard reference frame for the description of nucleic acid base-pair geometry Journal of Molecular Biology, 2001, 313 (1), 229-37. PubMed

	VS Reddy, P Natarajan, B Okerberg, K Li, KV Damodaran, RT Morton, CL Brooks, III and JE Johnson Virus Particle Explorer (VIPER), a website for virus capsid structures and their computational analyses Journal of Virology, 2001, 75 (24), 11943-7. PubMed

	G Ren, VS Reddy, A Cheng, P Melnyk and AK Mitra Visualization of a water-selective pore by electron crystallography in vitreous ice Proceedings of the National Academy of Sciences, USA, 2001, 98 (4), 1398-403 .

	O Roche, R Kiyama and CL Brooks, III Ligand-protein database: linking protein-ligand complex structures to binding data Journal of Medicinal Chemistry, 2001, 44 (22), 3592-8. PubMed

	KA Sharp and CL Brooks, III Theory and simulation Old wine in new bottles? Current Opinion in Structural Biology, 2001, 11 (2), 209-211 .

	CP Sosa, T Hewitt, MR Lee and DA Case Vectorization of the generalized Born model for molecular dynamics on shared-memory computers Journal of Molecular Structure (Theochem), 2001, 549 (193-201).

	L Tang, KN Johnson, LA Ball, T Lin, M Yeager and JE Johnson The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA Nature Structural Biology, 2001, 8 (1), 77-83. PubMed

	V Tsui and DA Case Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics Journal of Physical Chemistry B, 2001, 105, 11314-11325 .

	W Wriggers and P Chacon Using Situs for the Registration of Protein Structures with Low-Resolution Bead Models from X-ray Solution Scattering Journal of Applied Crystallography, 2001, 34, 773-776 .

	W Wriggers and S Birmanns Using situs for flexible and rigid-body fitting of multiresolution single-molecule data Journal of Structural Biology, 2001, 133 (2-3), 193-202. PubMed

	W Wriggers and P Chacon Modeling tricks and fitting techniques for multiresolution structures Structure (Camb), 2001, 9 (9), 779-88. PubMed

	2000

	Journal Articles

	D Bashford and DA Case Generalized Born models of macromolecular solvation effects Annual Reviews of Physical Chemistry, 2000, 51, 129-52. PubMed

	BD Bursulaya and CL Brooks, III Comparative Study of the Folding Free Energy Landscape of a Three-Stranded b-Sheet Protein with Explicit and Implicit Solvent Models Journal of Physical Chemistry B, 2000, 104 (51), 12378-12383 .

	MA Canady, M Tihova, TN Hanzlik, JE Johnson and M Yeager Large conformational changes in the maturation of a simple RNA virus, nudaurelia capensis omega virus (NomegaV) Journal of Molecular Biology, 2000, 299 (3), 573-84. PubMed

	M Feig, P Rotkiewicz, A Kolinski, J Skolnick and CL Brooks, III Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models Proteins: Structure, Function, and Genetics, 2000, 41 (1), 86-97. PubMed

	E Kim, W Wriggers, M Phillips, K Kokabi, PA Rubenstein and E Reisler Cross-linking constraints on F-actin structure Journal of Molecular Biology, 2000, 299 (2), 421-9. PubMed

	J-E Shea, JN Onuchic and CL Brooks, III Energetic frustration and the nature of the transition state in protein folding Journal of Chemical Physics, 2000, 113 (17), 7663-7671 .

	C Simmerling, M Lee, AR Ortiz, A Kolinski, J Skolnick and PA Kollman Combining MONSSTER and LES/PME to predict protein structure from amino acid sequence: Application to the small protein CMTI-1 Journal of the Americal Chemical Society, 2000, 122 (35), 8392-8402 .

	MC Sousa, CB Trame, H Tsuruta, SM Wilbanks, VS Reddy and DB McKay Crystal and solution structures of an HslUV protease-chaperone complex Cell, 2000, 103 (4), 633-43 .

	V Tsui and DA Case Molecular dynamics simulations of nucleic acids with a generalized Born solvation model. Journal of the Americal Chemical Society, 2000, 122, 2489-2498 .

	A Van der Vaart, BD Bursulaya, CL Brooks, III and KM Merz, Jr. Are Many-Body Effects Important in Protein Folding? Journal of Physical Chemistry B, 2000, 104 (40), 9554-9563 .

	J Xing, W Wriggers, GM Jefferson, R Stein, HC Cheung and SS Rosenfeld Kinesin has three nucleotide-dependent conformations. Implications for strain-dependent release Journal of Biological Chemistry, 2000, 275 (45), 35413-23. PubMed

	Book Chapters

	MS Van Loock, A Malhotra, DA Case, R Agrawal, P Penczek, TR Easterwood, J Frank and SC Harvey A functional interpretation of the cryo-electron microscopy map of the 30S ribosomal subunit from Escherichai coli The Ribsome, 2000, RA Garret, SR Douthwaite, A Liljas, AT Matheson, PB Moore andHF Noller, ASM press, Washington DC, Pgs 165-171.

	1999

	Journal Articles

	BN Dominy and CL Brooks, III Development of a Generalized Born Model Parametrization for Proteins and Nucleic Acids Journal of Physical Chemistry B, 1999, 103 (18), 3765-3773 .

	BA Harris and SC Harvey Program for analyzing knots represented by polygonal paths Journal of Computational Chemistry, 1999, 20, 813-818 .

	A Kolinski, B Ilkowski and J Skolnick Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques Biophysical Journal, 1999, 77 (6), 2942-52. PubMed

	MA Krol, NH Olson, J Tate, JE Johnson, TS Baker and P Ahlquist RNA-controlled polymorphism in the in vivo assembly of 180-subunit and 120-subunit virions from a single capsid protein. Proceedings of the National Academy of Sciences, USA, 1999, 96, 13650-13655 .

	D Mohanty, A Kolinski and J Skolnick De novo simulations of the folding thermodynamics of the GCN4 leucine zipper Biophysical Journal, 1999, 77 (1), 54-69. PubMed

	D Mohanty, BN Dominy, A Kolinski, CL Brooks, III and J Skolnick Correlation between knowledge-based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper Proteins: Structure, Function, and Genetics, 1999, 35 (4), 447-52. PubMed

	AR Ortiz, A Kolinski, P Rotkiewicz, B Ilkowski and J Skolnick CASP3 Proceedings: Ab inito folding of proteins using restraints derived from evolutionary information Proteins: Structure, Function, and Genetics - Supplement, 1999, 3, 177-185 .

	AR Ortiz, A Kolinski, P Rotkiewicz, B Ilkowski and J Skolnick Ab Initio Folding of Proteins Using Restraints Derived from Evolutionary Information Proteins: Structure, Function, and Genetics, 1999, 3, 177-185 .

	D Rapaport, JE Johnson and J Skolnick Supramolecular self-assembly: Molecular dynamics modeling of polyhedral shell formation Computer Physics Communications, 1999, 121 (231-235).

	JE Shea, JN Onuchic and CL Brooks, III Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A Proceedings of the National Academy of Sciences, USA, 1999, 96 (22), 12512-7. PubMed

	J Skolnick, A Kolinski and D Mohanty De novo predicitons of the quaternary structure of leucine zippers and other coiled coils International Journal of Quantum Chemistry, 1999, 75 (165-176).

	J Srinivasan, MW Trevathan, P Beroza and DA Case Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects Theoretical Chemistry Accounts, 1999, 101, 426-434 .

	1998

	Journal Articles

	CL Brooks, III, M Gruebele, JN Onuchic and PG Wolynes Chemical physics of protein folding Proceedings of the National Academy of Sciences, USA, 1998, 95 (19), 11037-8. PubMed

	TE Cheatham, III, J Srinivasan, DA Case and PA Kollman Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution Journal of Biomolecular Structure and Dynamics, 1998, 16 (2), 265-80. PubMed

	AR Ortiz, A Kolinski and J Skolnick Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments Journal of Molecular Biology, 1998, 277 (2), 419-48. PubMed

	AR Ortiz, A Kolinski and J Skolnick Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments Proteins: Structure, Function, and Genetics, 1998, 30 (3), 287-94. PubMed

	AR Ortiz, A Kolinski and J Skolnick Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations Proceedings of the National Academy of Sciences, USA, 1998, 95 (3), 1020-5. PubMed

	VS Reddy, HA Giesing, RT Morton, A Kumar, CB Post, CL Brooks, III and JE Johnson Energetics of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses Biophysical Journal, 1998, 74 (1), 546-58. PubMed

	J Skolnick, A Kolinski and AR Ortiz Reduced protein models and their application to the protein folding problem Journal of Biomolecular Structure and Dynamics, 1998, 16, 381-396 .

	J Srinivasan, TE Cheatham, III, P Cieplak, PA Kollman and DA Case Continuum Solvent Studies of the Stability of DNA, RNA and Phosphoramidate-DNA Helices. Journal of the Americal Chemical Society, 1998, 120, 9401-9409 .

	J Srinivasan, J Miller, PA Kollman and DA Case Continuum solvent studies of the stability of RNA hairpin loops and helices Journal of Biomolecular Structure and Dynamics, 1998, 16 (3), 671-82. PubMed

	M Vieth, JD Hirst, A Kolinski and CL Brooks, III Assessing Energy Functions for Flexible Docking Journal of Computational Chemistry, 1998, 19, 1612-1622 .

	M Vieth, JD Hirst, A Kolinski and CL Brooks, III Assessing Search Strategies for Flexible Docking Journal of Computational Chemistry, 1998, 19, 1623-1631 .

	M Vieth, JD Hirst and CL Brooks, III Do active site conformations of small ligands correspond to low free-energy solution structures? Journal of Computer-Aided Molecular Design, 1998, 12 (6), 563-72. PubMed

	Book Chapters

	JE Johnson and VS Reddy Structural studies of nodaviruses and tetraviruses Insect Viruses, 1998, L Miller andL Ball, Plenum, New York, Pgs 171-223.

	AD MacKerell, Jr., BR Brooks, CL Brooks, III, L Nilsson, B Roux, Y Won and M Karplus CHARMM: The energy function and its parameterization Encyclopedia of Computational Chemistry, 1998, PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer, III andPR Schreiner, John Wiley & Sons, Ltd., Chichester, UK, Pgs 271-277.