Protein Structure Prediction Using a Combination of Sequence Homology and Global Energy Minimization: II. Energy Functions Dudek, Michael J. Ramnarayan, K. Ponder, Jay W.

An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments Yang AS, Honig B

Protein analyst--a distributed object environment for protein sequence and structure analysis Saqi MA, Wild DL, Hartshorn MJ

Modeling three-dimensional protein structures for amino acid sequences of the CASP3 experiment using sequence-derived predictions Fischer D

Homology modeling with low sequence identity Tramontano A

Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turns Hu WP, Kolinski A, Skolnick J

A structural census of the current population of protein sequences. Gerstein M, Levitt M

Protein v47 Issue S3, 1999 CASP3 supplement   Full text of all papers

The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999 Amos Bairoch and Rolf Apweiler
 

Homology Detection
Homology Detection Blocks-based methods for detecting protein homology Henikoff, J. G. Pietrokovski, S., Henikoff, S.

Statistical alignment: computational properties, homology testing and goodness-of-fit Hein J, Wiuf C, Knudsen B, Moller MB, Wibling G

A New Algorithm for Analysis of the Homology in Protein Primary Structure Leluk,

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs SF Altschul, TL Madden, AA Schaffer, J Zhang, Z Zhang, W Miller, and DJ Lipman

Sensitivity and selectivity in protein similarity searches: a comparison of Smith-Waterman in hardware to BLAST and FASTA Shpaer EG, Robinson M, Yee D, Candlin JD, Mines R, Hunkapiller T
 

Alignment
Accurate formula for P-values of gapped local sequence and profile alignments Mott R

Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment Heringa J

Structure-based evaluation of sequence comparison and fold recognition alignment accuracy Domingues FS, Lackner P, Andreeva A, Sippl MJ

Homology-based Method for Identification of Protein Repeats Using Statistical Significance Estimates Andrade, M.A. Ponting, C.P. Bork, P.

Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions P Briffeuil, G Baudoux, C Lambert, X De Bolle, C Vinals, E Feytmans, and
E Depiereux
 

Secondary Structure
An approach to improving multiple alignments of protein sequences using predicted secondary structure Andrew J. Jennings1,2, Colin M. Edge1 and Michael J.E. Sternberg

(for PCK) Seventy-five percent accuracy in protein secondary structure prediction Frishman D, Argos P
 

Folds
A systematic comparison of protein structure classifications: SCOP, CATH and FSSP Hadley C, Jones DT

CATH--a hierarchic classification of protein domain structures Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM.

Protein folding: from the levinthal paradox to structure prediction Honig B.

Structure classification-based assessment of CASP3 predictions for the fold recognition targets  Alexey G. Murzin

Protein folds and families: sequence and structure alignments L Holm and C Sander

Examples
*Structure of the human glycogen-associated protein phosphatase 1 regulatory subunit hGM: Homology modeling revealed an(alpha/beta)8-barrel-like fold in the multidomain protein Souchet, Michel Legave, Marie-Noelle Berrebi-Bertrand, Isabelle

*Homology modeling and active-site residues probing of the thermophilic Alicyclobacillus acidocaldarius esterase 2 Manco, Giuseppe Febbraio, Ferdinando Rossi,Mose

Analysis of the relation between the sequence and secondary and three-dimensional structures of immunoglobulin molecules Gelfand IM, Kister AE

Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments Sahasrabudhe PV, Tejero R, Kitao S, Furuichi Y, Montelione GT

Linking CoMFA and protein homology models of enzyme-inhibitor interactions: an application to non-steroidal aromatase inhibitors Cavalli A, Greco G, Novellino E, Recanatini M.

Comparative model building of interleukin-7 using interleukin-4 as a template: a structural hypothesis that displays atypical surface chemistry in helix D important for receptor activation Cosenza L, Rosenbach A, White JV, Murphy JR, Smith T.

Three-dimensional models of estrogen receptor ligand binding domain complexes, based on related crystal structures and mutational and structure-activity relationship data Wurtz JM, Egner U, Heinrich N, Moras D, Mueller-Fahrnow A.

Modeling based on the structure of vicilins predicts a histidine cluster in the active site of oxalate oxidase Gane PJ, Dunwell JM, Warwicker J.

A homology model for the human theta-class glutathione transferase T1-1 Flanagan JU, Rossjohn J, Parker MW, Board PG, Chelvanayagam G.

Homology model of the closed, functionally active, form of the amino terminal domain of mGlur1 Costantino G, Macchiarulo A, Pellicciari R.

*Protein Science from 1999 is no longer available.