Commits

Branch selector

 master

User selector

All users

Datepicker

All time

Commit History

Commits on Jan 20, 2023

• fix cpu only compile of test

  effectsToCause

  authored
  ebd265e

  Copy full SHA for ebd265e

Commits on Jan 13, 2023

• clear volume data at beginning of each energy calculation to simply avoid data collisions, at 12A cutoff to improve speed 2X at near zero accuracy cost

  effectsToCause

  committed
  d4e2927

  Copy full SHA for d4e2927

Commits on Jan 10, 2023

• need full matrix size to match up bonding conditions to be optimized at a later time

  effectsToCause

  authored
  a5acb22

  Copy full SHA for a5acb22

• only allocate necessary cuda cores and avoid minor redundancy

  effectsToCause

  authored
  8c7362c

  Copy full SHA for 8c7362c

Commits on Jan 9, 2023

• protEnergy: use final updated dielectric parameters for improved implementation

  effectsToCause

  committed
  aa82052

  Copy full SHA for aa82052

• protCAD: implementation of protEnergy, protMin and protRelax CUDA version and automatic compiliation support

  effectsToCause

  committed
  dd3553b

  Copy full SHA for dd3553b

Commits on Nov 17, 2022

• Reset alignment outlier cutoff between each trial

  effectsToCause

  authored
  d6a1ec7

  Copy full SHA for d6a1ec7

• Fix off by one bug in alignment slide

  effectsToCause

  authored
  413a246

  Copy full SHA for 413a246

Commits on Nov 15, 2022

• updates (#85)

  Show description for aa4a531
  effectsToCause

  authored
  aa4a531

  Copy full SHA for aa4a531

Commits on Oct 21, 2022

• protEvolver: fix possiblemutants.out generation bug (#84)

  effectsToCause

  authored
  fcbffeb

  Copy full SHA for fcbffeb

Commits on Oct 20, 2022

• Merge branch 'master' into master

  effectsToCause

  authored
  7e67e30

  Copy full SHA for 7e67e30

Commits on Jul 21, 2022

• Readme: cite VX paper

  effectsToCause

  committed
  c50878b

  Copy full SHA for c50878b

• General updates as well as adding zinc and zinc binding residues to forcefeild parameters, and cterminal methyle cap (NME) (#83)

  Show description for 304580c
  

  effectsToCause

  and

  Wildemujr

  authored
  304580c

  Copy full SHA for 304580c

• protMutator: update readme

  effectsToCause

  committed
  f7ba89b

  Copy full SHA for f7ba89b

• correct readme

  effectsToCause

  committed
  fe7c42a

  Copy full SHA for fe7c42a

• rm bin

  effectsToCause

  committed
  e5f101b

  Copy full SHA for e5f101b

• merge updates

  effectsToCause

  committed
  7702dcd

  Copy full SHA for 7702dcd

Commits on Dec 9, 2021

• updates

  effectsToCause

  committed
  dab7cec

  Copy full SHA for dab7cec

Commits on Nov 10, 2021

• protMutator: read input file with point mutation formatted input data

  effectsToCause

  committed
  ba7bfa3

  Copy full SHA for ba7bfa3

Commits on Sep 14, 2021

• protEvolver: make it resistant to cross-node rand collisions. protSampling: add intended to be run parallel replica exchange style simulation to span local conformational landscape

  effectsToCause

  committed
  b92ec72

  Copy full SHA for b92ec72

Commits on Sep 8, 2021

• protBindingEnergy: Don't calculate configuration entropy of peptide (or small molecule) in free unbound state

  effectsToCause

  committed
  d22912f

  Copy full SHA for d22912f

Commits on Sep 2, 2021

• protEnergy: added ability to predict TM by varying temperature effecting solvent and configuration entropy and find temperature energy crosses zero

  effectsToCause

  committed
  48f78b6

  Copy full SHA for 48f78b6

• Energy: implement RPT bin based configuration entropy term

  effectsToCause

  committed
  74054c8

  Copy full SHA for 74054c8

Commits on Aug 26, 2021

• protEvolver: revert sampling winnow method back to frequency based as it's most effective until another more precise method is employed

  effectsToCause

  committed
  6768410

  Copy full SHA for 6768410

Commits on Aug 23, 2021

• protEvolver: testing boltzmann based sampling winnowing

  effectsToCause

  committed
  5d57938

  Copy full SHA for 5d57938

Commits on Aug 9, 2021

• Merge branch 'dev' into master

  effectsToCause

  authored
  11cd72b

  Copy full SHA for 11cd72b

• Merge pull request #11 from protCAD/master

  Show description for 8f4c476
  effectsToCause

  authored
  8f4c476

  Copy full SHA for 8f4c476

• Merge branch 'master' into master

  effectsToCause

  authored
  5ad53e5

  Copy full SHA for 5ad53e5

• updates to master

  effectsToCause

  committed
  4360a7c

  Copy full SHA for 4360a7c

• protDihedrals: add resnum to print

  effectsToCause

  committed
  f318d42

  Copy full SHA for f318d42

Commits on Aug 6, 2021

• add RPT limited backbone sampling to clash clearing protocol (protRelax) as it is easier to jump energy hurdles and is much faster. Also remove protFolder from makefile targets as it needs signific…

  Show description for 3beed76
  effectsToCause

  committed
  3beed76

  Copy full SHA for 3beed76

Commits on Aug 4, 2021

• correct rand sidechain conformation range

  effectsToCause

  committed
  0c70de3

  Copy full SHA for 0c70de3

• clash clearing continues to use rotamers, minimization (protMin) uses a random one degree increment around a thirty degree range of current sidechain dihedral

  effectsToCause

  committed
  17dec32

  Copy full SHA for 17dec32

• cleanup some warnings

  effectsToCause

  committed
  493393f

  Copy full SHA for 493393f

• add missing nterminal TYR data files

  effectsToCause

  committed
  7407e6d

  Copy full SHA for 7407e6d

Pagination

Previous

Next