rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny
M. W. Dimmic, J. S. Rest, D. P. Mindell, and R. A. Goldstein
Journal of Molecular Evolution, submitted.

Optimization of a new score function for accurate alignment
B. Qian and R. A. Goldstein
Proteins, submitted.

Why are proteins so robust to site mutations?
D. Taverna and R. A. Goldstein
Journal of Molecular Biology, submitted.

Using evolutionary methods to study G-protein coupled receptors
O. Soyer, M. W. Dimmic, R. R. Neubig, and R.A. Goldstein
Pacific Symposium on Biocomputing , submitted.

Why are proteins marginally stable?
D. Taverna and R. A. Goldstein
Proteins, in press. [Abstract]

Evolutionary perspectives on protein structure, stability, and functionality
R. A. Goldstein
Proceedings of the International School of Physics "Enrico Fermi", in press.

The distribution of indel lengths
B. Qian and R. A. Goldstein
Proteins 45, (2001), 102-104. [Abstract, PDF (83 kB)]

Evolution of functionality in lattice proteins
P. D. Williams, D. D. Pollock, and R.A. Goldstein
Journal of Molecular Graphics and Modelling 19, (2001), 150-156. [Abstract, PDF (295 kB)]

Optimization of a new score function for the detection of remote homologs
M. Kann, B. Qian, and R.A. Goldstein
Proteins 41 (2000), 498-503. [Abstract, PDF (114 kB)]

How to Generate Improved Potentials for Protein Tertiary Structure Prediction:  A Lattice Model Study
T.-L. Chiu and R.A. Goldstein
Proteins 41 (2000), 157-163. [Abstract, PDF (126 kB)]

Optimizing for Success: A New Score Function For Distantly Related Protein Sequence Comparison
M. Kann and R.A. Goldstein
RECOMB 2000.
(Refereed conference proceeding), [Abstract, PDF (398 kB)]

Modeling Evolution at the Protein Level using an Adjustable Amino Acid Fitness Model
M.W. Dimmic, D. P. Mindell, and R.A. Goldstein
Pacific Symposium on Biocomputing 2000.
(Refereed conference proceeding), [Abstract, PDF (46 kB)]

The Evolution of Duplicated Genes Considering Protein Stability Constraints
D.M. Taverna and R.A. Goldstein
Pacific Symposium on Biocomputing 2000.
(Refereed conference proceeding), [Abstract, PDF (66 kB)]]

Surveying Determinants of Protein Structure Designability across Different Energy Models and Amino-Acid Alphabets: A Consensus
N.E.G. Buchler and R.A. Goldstein
Journal of Chemical Physics 112 (2000), 2533-2547. [Abstract, PDF (376 kB)]

The Distribution of Structures in Evolving Protein Populations
D.M. Taverna and R.A. Goldstein
Biopolymers 53, (2000), 1-8. [Abstract, PDF (99 kB)] 

Universal Correlation between Energy Gap and Foldability for the Random Energy Model and Lattice Proteins
N.E.G. Buchler and R.A. Goldstein
Journal of Chemical Physics 111 (1999), 6599-6609. [Abstract, PDF (241 kB)]

Estimating the Total Number of Protein Folds
S. Govindarajan, R. Recabarren, and R.A. Goldstein
Proteins 35 (1999), 408-414. [Abstract, PDF (118 kB)]

Using Physical-Chemistry Based Mutation Models in Phylogenetic Analyses of HIV-1 Subtypes
J.M Koshi, D.P. Mindell, and R.A. Goldstein
Molecular Biology and Evolution 16 (1999), 173-179. [Abstract, PDF (92 kB)]

The Effect of Alphabet Size and Foldability Requirements on Protein Structure Designability
N.E.G Buchler and R.A. Goldstein
Proteins 34 (1999), 113-124. [Abstract, PDF (237 kB)]

Optimizing Potentials for the Inverse Protein Folding Problem
T.-L. Chiu and R.A. Goldstein
Protein Engineering 11 (1998), 749-752. [Abstract, PDF (106 kB)]

Optimizing Energy Potentials for Success in Protein Tertiary Structure Prediction
T.-L. Chiu and R.A. Goldstein
Folding & Design 3 (1998), 223-228. [Abstract, PDF (319 kB)]

On the Thermodynamic Hypothesis of Protein Folding
S. Govindarajan and R.A. Goldstein
Proc. Nat'l Acad. Sci (USA) 95 (1998), 5545-5549. [Abstract, PDF (169 kB)]

Models of Natural Mutations Including Site Heterogeneity
J.M. Koshi and R.A. Goldstein
Proteins 32 (1998), 289-295. [Abstract, PDF (103 kB)]

Beyond Mutation Matrices: Physical-chemistry Based Evolutionary Models
J.M. Koshi, D.P. Mindell, and R.A. Goldstein
Genome Informatics 1997 (1998), refereed conference proceeding. [Abstract, PDF (225 kB)] 

Evolution of Model Proteins on a Foldability Landscape
S. Govindarajan and R.A. Goldstein
Proteins 29 (1997), 461-466 . [Abstract, PDF (75 kB)]

Site Mutations in Model Proteins
S. Govindarajan and R.A. Goldstein
Mathematical Modelling and Scientific Computing (1997), in press. [Abstract]

The Foldability Landscape of Model Proteins
S. Govindarajan and R.A. Goldstein
Biopolymers 42 (1997), 427-438. [Abstract, PDF (268 kB)]

Predicting Protein Secondary Structure Using Probabilistic Substitution Schemata
M.J. Thompson and R.A. Goldstein
Protein Science 6 (1997), 1963-1975. [Abstract, PDF (273 kB, manuscript, reprint available on request)]

Compaction and Folding in Model Proteins
T.-L. Chiu and R.A. Goldstein
Journal of Chemical Physics 107 (1997), 4408-4415. [Abstract, PDF (293 kB)]

Protein Heteronuclear NMR Assignments using Mean-Field Simulated Annealing
N.E.G. Buchler, E.R.P. Zuiderweg, H. Wang, and R.A. Goldstein
Journal of Magnetic Resonance 125 (1997), 34-42. [Abstract, PDF (665 kB)] 

Mutation Matrices and Physical-Chemical Properties: Correlations and Implications
J.M. Koshi and R.A. Goldstein
Proteins 27 (1996), 336-344. [Abstract, PDF (84 kB)]

Probabilistic Reconstruction of Ancestral Protein Sequences
J.M. Koshi and R.A. Goldstein
Journal of Molecular Evolution 42 (1996), 313-320. [Abstract, PDF (352 kB)]

Why are some Protein Structures so Common?
S. Govindarajan and R.A. Goldstein
Proc. Nat'l Acad. Sci (USA) 93 (1996), 3341-3345. [Abstract, PDF (174 kB)]

Predicting Solvent Accessibility: Higher Accuracy Using Bayesian Statistics and Optimized Residue Substitution Classes
M.J. Thompson and R.A. Goldstein
Proteins 25 (1996), 38-47. [Abstract (reprint available on request)]

Constructing Amino Acid Residue Substitution Classes Maximally Indicative of Local Protein Structure
M.J. Thompson and R.A. Goldstein
Proteins 25 (1996), 28-37. [Abstract (reprint available on request)] 

Correlating Structure-Dependent Mutation Matrices with Physical-Chemical Properties
J.M. Koshi and R.A. Goldstein
Pacific Symposium on Biocomputing '96, (L. Hunter and T. E. Klein eds) (1995), 488-499. World Scientific, Singapore. [Abstract (reprint available on request)]

Optimal Local Propensities for Model Proteins
S. Govindarajan and R.A. Goldstein
Proteins 22 (1995), 413-418. [Abstract (reprint available on request)]

Context-Dependent Optimal Substitution Matrices Derived Using Bayesian Statistics and Phylogenetic Trees
J.M. Koshi and R.A. Goldstein
Protein Engineering 8 (1995), 641-645. [Abstract (reprint available on request)]

Searching for Foldable Protein Structures using Optimized Energy Functions
S. Govindarajan and R.A. Goldstein
Biopolymers 36 (1995), 43-51. [Abstract (reprint available on request)] 

Optimized Energy Functions for Tertiary Structure Prediction and Recognition
R.A. Goldstein, Z.A. Luthey-Schulten, and P.G. Wolynes
Protein Structure by Distance Analysis (1994), 135-144. IOS Press, Amsterdam. [Abstract (reprint available on request)]

3-Dimensional Model for the Hormone-Binding Domains of Steroid-Receptors
R.A. Goldstein, J.A. Katzenellenbogen, Z.A. Luthey-Schulten, D.A. Seielstad, and P.G. Wolynes
Proc. Nat'l Acad. Sci (USA) 90 (1993), 9949-9953. [Abstract, PDF (1143 kB)]

Protein Tertiary Structure Prediction using Optimized Hamiltonians with Local Interactions
R.A. Goldstein, Z.A. Luthey-Schulten, and P.G. Wolynes
Proc. Nat'l Acad. Sci (USA) 89 (1992), 9029-9033. [Abstract, PDF (1031 kB)]

Optimal Protein-Folding Codes from Spin-Glass Theory
R.A. Goldstein, Z.A. Luthey-Schulten, and P.G. Wolynes
Proc. Nat'l Acad. Sci (USA) 89 (1992), 4918-4922. [Abstract, PDF (1010 kB)]

Generalized Protein Tertiary Structure Recognition using Associative Memory Hamiltonians
M.S. Friedrichs, R.A. Goldstein, and P.G. Wolynes
Journal of Molecular Biology 222 (1991), 1013-1034.

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