R. Amaro

Molecular Biology · 2005–2021

A researcher in the Science corpus: 8 papers; trusts 10 researchers and is trusted by 6 researchers here, as inferred from the citation graph.

Subfields

• Molecular Biology — 89 citations into it; #6,175 of 17,773 by trust here, #7,041 by citations
• Computational Theory and Mathematics — 56 citations into it; #5,567 of 12,182 by trust here, #1,667 by citations
• Materials Chemistry — 36 citations into it
• Computational Chemistry & Drug Discovery — 35 citations into it
• Organic Chemistry — 20 citations into it
• Radiology, Nuclear Medicine and Imaging — 10 citations into it
• Pharmacology — 8 citations into it

Whom R. Amaro trusts overall

Their strongest outbound trust, strongest first, inferred from their citations.

1. W. L. Jorgensen
2. John J. Irwin
3. Sérgio Filipe Sousa
4. Gisbert Schneider
5. A. W. Schüttelkopf

Who trusts R. Amaro overall

1. Jacob D. Durrant
2. Antonio Lavecchia
3. James Andrew McCammon
4. W. Sinko
5. S. J. Macalino
6. Sandro Cosconati
7. Steffen Lindert
8. C. D. Giovanni
9. Michael J. Wasko
10. Vijayakumar Gosu

Papers from R. Amaro's perspective

Ordered by how strongly the researchers R. Amaro trusts endorse each paper. Same corpus, a different order for every researcher.

1. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading
2. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
3. Comparative study of several algorithms for flexible ligand docking (J. Comput. Aided Mol. Des.)
4. Highly accurate protein structure prediction with AlphaFold
5. Virtual Computational Chemistry Laboratory – Design and Description
6. A fast flexible docking method using an incremental construction algorithm.
7. Protein–ligand docking: Current status and future challenges
8. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.
9. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties.
10. Protein complex prediction with AlphaFold-Multimer

Their papers

• D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies (2019) — 113 citations
• Reaction coupling through interdomain contacts in imidazole glycerol phosphate synthase. (2005) — 53 citations
• An improved relaxed complex scheme for receptor flexibility in computer-aided drug design (2008) — 323 citations
• D3R Grand Challenge 2: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies (2017) — 173 citations
• AutoGrow: A Novel Algorithm for Protein Inhibitor Design (2009) — 112 citations
• CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding (2021) — 83 citations
• Ensemble Docking in Drug Discovery. (2018) — 412 citations
• Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein (2020) — 829 citations