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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 70,658 bioRxiv papers from 308,473 authors.

Author: John D. Chodera

Rankings

  • All-time downloads: 23,652 (rank: 1,075 out of 308,421)
  • Categories:
    • biochemistry: 3,152 (rank: 170 out of 12,506)
    • bioinformatics: 1,300 (rank: 6,680 (tie) out of 26,841)
    • biophysics: 15,779 (rank: 21 out of 12,362)
    • cancer biology: 2,044 (rank: 1,149 (tie) out of 20,067)
    • pharmacology and toxicology: 1,377 (rank: 156 (tie) out of 3,754)

Downloads per author, site-wide

Preprints

Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge

biophysics more details view paper

No bioRxiv download data for this paper yet.

Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1

biophysics more details view paper
  • Downloaded 2,905 times
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    • Site-wide: 1,329 out of 70,653
    • In biophysics: 31 out of 3,010
  • Year to date:
    • Site-wide: 1,663 out of 70,653
  • Since beginning of last month:
    • Site-wide: 5,301 out of 70,653

A simple method for automated equilibration detection in molecular simulations

biophysics more details view paper
  • Downloaded 2,213 times
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    • Site-wide: 2,159 out of 70,653
    • In biophysics: 52 out of 3,010
  • Year to date:
    • Site-wide: 11,710 out of 70,653
  • Since beginning of last month:
    • Site-wide: 18,728 out of 70,653

An open library of human kinase domain constructs for automated bacterial expression

biochemistry more details view paper
  • Downloaded 1,817 times
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    • Site-wide: 3,033 out of 70,653
    • In biochemistry: 57 out of 2,120
  • Year to date:
    • Site-wide: 9,055 out of 70,653
  • Since beginning of last month:
    • Site-wide: 18,246 out of 70,653

The Dynamic Conformational Landscapes of the Protein Methyltransferase SETD8

biophysics more details view paper
  • Downloaded 1,612 times
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    • Site-wide: 3,719 out of 70,653
    • In biophysics: 97 out of 3,010
  • Year to date:
    • Site-wide: 17,490 out of 70,653
  • Since beginning of last month:
    • Site-wide: 37,626 out of 70,653

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

pharmacology and toxicology more details view paper
  • Downloaded 1,377 times
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    • Site-wide: 4,881 out of 70,653
    • In pharmacology and toxicology: 22 out of 598
  • Year to date:
    • Site-wide: 8,812 out of 70,653
  • Since beginning of last month:
    • Site-wide: 19,092 out of 70,653

Ensembler: Enabling high-throughput molecular simulations at the superfamily scale

bioinformatics more details view paper
  • Downloaded 1,300 times
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    • Site-wide: 5,357 out of 70,653
    • In bioinformatics: 1,021 out of 6,919
  • Year to date:
    • Site-wide: 31,905 out of 70,653
  • Since beginning of last month:
    • Site-wide: 26,807 out of 70,653

Quantifying configuration-sampling error in Langevin simulations of complex molecular systems

biophysics more details view paper
  • Downloaded 1,291 times
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    • Site-wide: 5,408 out of 70,653
    • In biophysics: 154 out of 3,010
  • Year to date:
    • Site-wide: 9,829 out of 70,653
  • Since beginning of last month:
    • Site-wide: 28,341 out of 70,653

OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics

biophysics more details view paper
  • Downloaded 1,281 times
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    • Site-wide: 5,478 out of 70,653
    • In biophysics: 157 out of 3,010
  • Year to date:
    • Site-wide: 15,087 out of 70,653
  • Since beginning of last month:
    • Site-wide: 24,778 out of 70,653

Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia

cancer biology more details view paper
  • Downloaded 1,095 times
  • Download rankings, all-time:
    • Site-wide: 7,142 out of 70,653
    • In cancer biology: 189 out of 2,403
  • Year to date:
    • Site-wide: 31,246 out of 70,653
  • Since beginning of last month:
    • Site-wide: 41,033 out of 70,653

Biomolecular simulations under realistic macroscopic salt conditions

biophysics more details view paper
  • Downloaded 1,038 times
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    • Site-wide: 7,783 out of 70,653
    • In biophysics: 226 out of 3,010
  • Year to date:
    • Site-wide: 24,061 out of 70,653
  • Since beginning of last month:
    • Site-wide: 13,946 out of 70,653

Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations

cancer biology more details view paper
  • Downloaded 949 times
  • Download rankings, all-time:
    • Site-wide: 9,056 out of 70,653
    • In cancer biology: 257 out of 2,403
  • Year to date:
    • Site-wide: 11,942 out of 70,653
  • Since beginning of last month:
    • Site-wide: 11,680 out of 70,653

Avoiding accuracy-limiting pitfalls in the study of protein-ligand interactions with isothermal titration calorimetry

biochemistry more details view paper
  • Downloaded 909 times
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    • Site-wide: 9,649 out of 70,653
    • In biochemistry: 178 out of 2,120
  • Year to date:
    • Site-wide: 22,550 out of 70,653
  • Since beginning of last month:
    • Site-wide: 21,716 out of 70,653

The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations

biophysics more details view paper
  • Downloaded 902 times
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    • Site-wide: 9,768 out of 70,653
    • In biophysics: 283 out of 3,010
  • Year to date:
    • Site-wide: 885 out of 70,653
  • Since beginning of last month:
    • Site-wide: 3,730 out of 70,653

OpenPathSampling: A Python framework for path sampling simulations. I. Basics

biophysics more details view paper
  • Downloaded 845 times
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    • Site-wide: 10,875 out of 70,653
    • In biophysics: 334 out of 3,010
  • Year to date:
    • Site-wide: 6,641 out of 70,653
  • Since beginning of last month:
    • Site-wide: 19,730 out of 70,653

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge

biophysics more details view paper
  • Downloaded 764 times
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    • Site-wide: 12,610 out of 70,653
    • In biophysics: 395 out of 3,010
  • Year to date:
    • Site-wide: 17,592 out of 70,653
  • Since beginning of last month:
    • Site-wide: 31,276 out of 70,653

Overview of the SAMPL6 host-guest binding affinity prediction challenge

biophysics more details view paper
  • Downloaded 725 times
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    • Site-wide: 13,601 out of 70,653
    • In biophysics: 441 out of 3,010
  • Year to date:
    • Site-wide: 16,157 out of 70,653
  • Since beginning of last month:
    • Site-wide: 17,006 out of 70,653

pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments

biophysics more details view paper
  • Downloaded 717 times
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    • Site-wide: 13,852 out of 70,653
    • In biophysics: 450 out of 3,010
  • Year to date:
    • Site-wide: 11,796 out of 70,653
  • Since beginning of last month:
    • Site-wide: 7,609 out of 70,653

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

biophysics more details view paper
  • Downloaded 487 times
  • Download rankings, all-time:
    • Site-wide: 23,513 out of 70,653
    • In biophysics: 871 out of 3,010
  • Year to date:
    • Site-wide: 33,178 out of 70,653
  • Since beginning of last month:
    • Site-wide: 45,878 out of 70,653

Modeling error in experimental assays using the bootstrap principle: Understanding discrepancies between assays using different dispensing technologies

biochemistry more details view paper
  • Downloaded 426 times
  • Download rankings, all-time:
    • Site-wide: 27,441 out of 70,653
    • In biochemistry: 684 out of 2,120
  • Year to date:
    • Site-wide: 36,404 out of 70,653
  • Since beginning of last month:
    • Site-wide: 67,359 out of 70,653

Octanol-water partition coefficient measurements for the SAMPL6 Blind Prediction Challenge

biophysics more details view paper
  • Downloaded 375 times
  • Download rankings, all-time:
    • Site-wide: 31,570 out of 70,653
    • In biophysics: 1,244 out of 3,010
  • Year to date:
    • Site-wide: 6,873 out of 70,653
  • Since beginning of last month:
    • Site-wide: 4,489 out of 70,653

A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation

biophysics more details view paper
  • Downloaded 318 times
  • Download rankings, all-time:
    • Site-wide: 37,087 out of 70,653
    • In biophysics: 1,480 out of 3,010
  • Year to date:
    • Site-wide: 42,799 out of 70,653
  • Since beginning of last month:
    • Site-wide: 18,878 out of 70,653

OpenPathSampling: A Python framework for path sampling simulations. II. Building and customizing path ensembles and sample schemes

biophysics more details view paper
  • Downloaded 306 times
  • Download rankings, all-time:
    • Site-wide: 38,312 out of 70,653
    • In biophysics: 1,537 out of 3,010
  • Year to date:
    • Site-wide: 46,025 out of 70,653
  • Since beginning of last month:
    • Site-wide: 55,621 out of 70,653

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