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Protein structure comparison

Protein 3D Structure Computed from Evolutionary Sequence Variation

Debora S. Marks, Lucy J. Colwell, [ ... ], Chris Sander

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin

Predicting the Functional Effect of Amino Acid Substitutions and Indels

Yongwook Choi, Gregory E. Sims, [ ... ], Agnes P. Chan

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

Vincent Ranwez, Sébastien Harispe, Frédéric Delsuc, Emmanuel J. P. Douzery

Systematic Validation of Protein Force Fields against Experimental Data

Kresten Lindorff-Larsen, Paul Maragakis, [ ... ], David E. Shaw

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

Julie D. Thompson, Benjamin Linard, Odile Lecompte, Olivier Poch

Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?

Natalie Ward, Gabriel Moreno-Hagelsieb

Comparative Genomics of Flowering Time Pathways Using Brachypodium distachyon as a Model for the Temperate Grasses

Janet A. Higgins, Paul C. Bailey, David A. Laurie

Why Does the Giant Panda Eat Bamboo? A Comparative Analysis of Appetite-Reward-Related Genes among Mammals

Ke Jin, Chenyi Xue, [ ... ], Yufang Zheng

The Nod-Like Receptor (NLR) Family: A Tale of Similarities and Differences

Martina Proell, Stefan J. Riedl, [ ... ], Robert Schwarzenbacher

Beyond Reasonable Doubt: Evolution from DNA Sequences

W. Timothy J. White, Bojian Zhong, David Penny

Prediction of Metal Ion–Binding Sites in Proteins Using the Fragment Transformation Method

Chih-Hao Lu, Yu-Feng Lin, Jau-Ji Lin, Chin-Sheng Yu

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

V. Joachim Haupt, Simone Daminelli, Michael Schroeder

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